Variant report

Variant	rs1052930
Chromosome Location	chr3:20212189-20212190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20210669..20212300-chr3:20217697..20220649,2	K562	blood:
2	chr3:20211282..20213997-chr3:20225429..20228054,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PP2D1-2	chr3:20211553-20212307	NONHSAT088614

Variant related genes	Relation type
ENSG00000129810	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1061636	1.00[JPT][hapmap]
rs1124376	1.00[JPT][hapmap]
rs11712709	1.00[JPT][hapmap]
rs17006610	1.00[JPT][hapmap]
rs17006623	1.00[JPT][hapmap]
rs17797343	1.00[JPT][hapmap]
rs1828080	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs1848322	1.00[ASN][1000 genomes]
rs1848323	1.00[ASN][1000 genomes]
rs1868	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1995722	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2661378	0.85[CHD][hapmap]
rs2686313	0.85[CHD][hapmap]
rs2686314	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs2686316	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2686317	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs3828352	1.00[JPT][hapmap]
rs3852067	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4364184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4435663	0.83[CHD][hapmap];1.00[YRI][hapmap]
rs4491921	1.00[ASN][1000 genomes]
rs4858158	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4858769	1.00[YRI][hapmap]
rs4858778	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57625405	1.00[ASN][1000 genomes]
rs6419828	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6550307	1.00[JPT][hapmap]
rs6550373	0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.88[ASN][1000 genomes]
rs6550374	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6550402	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6550403	1.00[ASN][1000 genomes]
rs6550410	1.00[ASN][1000 genomes]
rs6550412	1.00[ASN][1000 genomes]
rs6550423	0.80[AMR][1000 genomes]
rs6767049	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6771941	1.00[JPT][hapmap]
rs6773807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6774367	1.00[JPT][hapmap]
rs6777450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6791385	1.00[JPT][hapmap]
rs6793304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796884	1.00[ASN][1000 genomes]
rs6809221	0.94[ASN][1000 genomes]
rs7619317	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7624514	0.85[CHD][hapmap]
rs7628915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635559	1.00[ASN][1000 genomes]
rs9310613	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9310615	0.83[EUR][1000 genomes]
rs951455	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs955011	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970589	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs978928	1.00[ASN][1000 genomes]
rs9810567	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9849205	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
20	nsv1013532	chr3:20172889-20305612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
21	nsv536513	chr3:20172889-20305612	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
22	esv1831289	chr3:20191506-20617984	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
23	esv1829973	chr3:20192578-20375260	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
24	esv1829847	chr3:20196923-20638228	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
25	nsv876597	chr3:20197364-20242143	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	esv1829457	chr3:20200232-20375260	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	esv1830113	chr3:20200232-20430932	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
28	esv3377463	chr3:20203472-20343029	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	esv3381923	chr3:20203492-20342999	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
30	esv1793845	chr3:20207023-20219694	Weak transcription Strong transcription Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1052930	UBE2E2	cis	parietal	SCAN
rs1052930	SGOL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:20167800-20226000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:20184600-20220200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:20188400-20212400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:20190600-20220200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:20192800-20220600	Weak transcription	Fetal Lung	lung
7	chr3:20193800-20226600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:20194000-20220400	Weak transcription	NH-A	brain
9	chr3:20194800-20215200	Weak transcription	HepG2	liver
10	chr3:20195000-20212400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:20195000-20226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:20195200-20221800	Weak transcription	NHEK	skin
13	chr3:20195400-20226000	Weak transcription	NHDF-Ad	bronchial
14	chr3:20195400-20226200	Weak transcription	NHLF	lung
15	chr3:20196400-20225600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:20196800-20221600	Weak transcription	Fetal Intestine Small	intestine
17	chr3:20197000-20226200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:20197000-20226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:20197400-20227000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:20197600-20226800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:20198200-20219800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:20198600-20220200	Weak transcription	Thymus	Thymus
23	chr3:20199400-20225400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:20199600-20221000	Weak transcription	Fetal Stomach	stomach
25	chr3:20199600-20225400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:20200000-20225800	Weak transcription	Osteobl	bone
27	chr3:20201800-20220000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:20201800-20225800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:20202600-20215600	Weak transcription	GM12878-XiMat	blood
30	chr3:20202600-20216200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:20202600-20226400	Weak transcription	Fetal Intestine Large	intestine
32	chr3:20203800-20215400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:20203800-20215600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:20205200-20225400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:20205800-20215600	Weak transcription	HUVEC	blood vessel
36	chr3:20205800-20225600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:20206600-20225400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:20207000-20223800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:20207200-20225600	Weak transcription	Primary B cells from cord blood	blood
40	chr3:20207600-20212400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:20208600-20225200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:20209400-20223800	Strong transcription	Dnd41	blood
43	chr3:20209600-20212600	Strong transcription	K562	blood
44	chr3:20209600-20225000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:20209600-20225200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr3:20209800-20213000	Strong transcription	Fetal Thymus	thymus
47	chr3:20210200-20212800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:20210400-20212200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:20210600-20212600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:20210600-20213400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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