Variant report

Variant	rs9828909
Chromosome Location	chr3:20212796-20212797
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20211282..20213997-chr3:20225429..20228054,3	MCF-7	breast:
2	chr3:20212661..20217850-chr3:20224065..20229766,9	K562	blood:

Variant related genes	Relation type
ENSG00000129810	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10514674	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10865760	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1122134	0.82[EUR][1000 genomes]
rs11713727	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11717832	0.94[EUR][1000 genomes]
rs11717876	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs1395985	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs1565192	0.84[EUR][1000 genomes]
rs17006708	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17006724	0.87[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1828079	0.85[MEX][hapmap];0.83[YRI][hapmap]
rs2089495	0.81[ASN][1000 genomes]
rs4858162	0.83[EUR][1000 genomes]
rs4858773	0.94[EUR][1000 genomes]
rs55919884	0.94[EUR][1000 genomes]
rs56296022	0.93[EUR][1000 genomes]
rs58070551	0.94[EUR][1000 genomes]
rs58780300	0.93[EUR][1000 genomes]
rs58959589	0.94[EUR][1000 genomes]
rs59527607	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59581357	0.94[EUR][1000 genomes]
rs60290831	0.94[EUR][1000 genomes]
rs6771625	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6774000	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6792484	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs73175204	0.94[EUR][1000 genomes]
rs73175210	0.94[EUR][1000 genomes]
rs73175211	0.94[EUR][1000 genomes]
rs977162	0.86[CEU][hapmap];0.90[TSI][hapmap]
rs9835099	0.93[EUR][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
rs9828909	RABGEF1	trans	parietal	SCAN
rs9828909	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	chr3:20190600-20220200	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:20192800-20220600	Weak transcription	Fetal Lung	lung
6	chr3:20193800-20226600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:20194000-20220400	Weak transcription	NH-A	brain
8	chr3:20194800-20215200	Weak transcription	HepG2	liver
9	chr3:20195000-20226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:20195200-20221800	Weak transcription	NHEK	skin
11	chr3:20195400-20226000	Weak transcription	NHDF-Ad	bronchial
12	chr3:20195400-20226200	Weak transcription	NHLF	lung
13	chr3:20196400-20225600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:20196800-20221600	Weak transcription	Fetal Intestine Small	intestine
15	chr3:20197000-20226200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:20197000-20226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:20197400-20227000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:20197600-20226800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:20198200-20219800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:20198600-20220200	Weak transcription	Thymus	Thymus
21	chr3:20199400-20225400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:20199600-20221000	Weak transcription	Fetal Stomach	stomach
23	chr3:20199600-20225400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:20200000-20225800	Weak transcription	Osteobl	bone
25	chr3:20201800-20220000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:20201800-20225800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:20202600-20215600	Weak transcription	GM12878-XiMat	blood
28	chr3:20202600-20216200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:20202600-20226400	Weak transcription	Fetal Intestine Large	intestine
30	chr3:20203800-20215400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:20203800-20215600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:20205200-20225400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:20205800-20215600	Weak transcription	HUVEC	blood vessel
34	chr3:20205800-20225600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:20206600-20225400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:20207000-20223800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:20207200-20225600	Weak transcription	Primary B cells from cord blood	blood
38	chr3:20208600-20225200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:20209400-20223800	Strong transcription	Dnd41	blood
40	chr3:20209600-20225000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:20209600-20225200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr3:20209800-20213000	Strong transcription	Fetal Thymus	thymus
43	chr3:20210200-20212800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:20210600-20213400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:20210800-20213600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:20210800-20213800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:20210800-20217200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:20211200-20215000	Weak transcription	HSMM	muscle
49	chr3:20211400-20220200	Weak transcription	Hela-S3	cervix
50	chr3:20211600-20215000	Weak transcription	A549	lung

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