Variant report

Variant	rs6722814
Chromosome Location	chr2:112811082-112811083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:112811043-112812168	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:112811029-112812327	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:112811039-112812152	HepG2	liver:	n/a	n/a
4	BHLHE40	chr2:112811032-112812172	K562	blood:	n/a	n/a
5	POLR2A	chr2:112810872-112812165	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr2:112811057-112811431	SH-SY5Y	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:112811068-112811118	Hepatocyte	liver:	n/a
2	chr2:112811068-112811118	GM06990	blood:	n/a
3	chr2:112811068-112811118	T-47D	breast:	n/a
4	chr2:112811068-112811118	NHBE	bronchial:	n/a
5	chr2:112811068-112811118	SKMC	muscle:	n/a
6	chr2:112811068-112811118	A549	lung:	n/a
7	chr2:112811068-112811118	K562	blood:	n/a
8	chr2:112811068-112811118	MCF-7	breast:	n/a
9	chr2:112811068-112811118	PrEC	prostate:	n/a
10	chr2:112811068-112811118	HPAEpiC	pulmonary alveolar:	n/a
11	chr2:112811068-112811118	HRPEpiC	eye:	n/a
12	chr2:112811068-112811118	HEK293	kidney:	embryo
13	chr2:112811068-112811118	ovcar-3	ovarian:	n/a
14	chr2:112811068-112811118	LNCaP	prostate:	n/a
15	chr2:112811068-112811118	GM12892	blood:	n/a
16	chr2:112811068-112811118	BE2_C	brain:	n/a
17	chr2:112811068-112811118	HEEpiC	esophagus:	n/a
18	chr2:112811068-112811118	HRCEpiC	kidney:	n/a
19	chr2:112811068-112811118	AoSMC	blood vessel:	n/a
20	chr2:112811068-112811118	ProgFib	skin:	n/a
21	chr2:112811068-112811118	ECC-1	luminal epithelium:	n/a
22	chr2:112811068-112811118	RPTEC	kidney:	n/a
23	chr2:112811068-112811118	U87	brain:	n/a
24	chr2:112811068-112811118	NT2-D1	testis:	n/a
25	chr2:112811068-112811118	IMR90	lung:	fetal
26	chr2:112811068-112811118	GM12878	blood:	n/a
27	chr2:112811068-112811118	HUVEC	blood vessel:	n/a
28	chr2:112811068-112811118	PFSK-1	brain:	n/a
29	chr2:112811068-112811118	AG04450	lung:	fetal
30	chr2:112811068-112811118	HNPCEpiC	eye:	n/a
31	chr2:112811068-112811118	HCPEpiC	choroid plexus:	n/a
32	chr2:112811068-112811118	Jurkat	blood:	n/a
33	chr2:112811068-112811118	PANC-1	pancreas:	n/a
34	chr2:112811068-112811118	AG04449	skin:	fetal
35	chr2:112811068-112811118	SAEC	small airway:	n/a
36	chr2:112811068-112811118	HAEpiC	amniotic membrane:	n/a
37	chr2:112811068-112811118	HL-60	blood:	n/a
38	chr2:112811068-112811118	GM12891	blood:	n/a
39	chr2:112811068-112811118	NH-A	brain:	n/a
40	chr2:112811068-112811118	HCF	heart:	n/a
41	chr2:112811068-112811118	BJ	skin:	n/a
42	chr2:112811068-112811118	CMK	blood:	n/a
43	chr2:112811068-112811118	MCF10A-Er-Src	breast:	n/a
44	chr2:112811068-112811118	AG09319	gingival:	n/a
45	chr2:112811068-112811118	SK-N-MC	brain:	n/a
46	chr2:112811068-112811118	SK-N-SH_RA	brain:	n/a
47	chr2:112811068-112811118	NHDF-neo	bronchial:	n/a
48	chr2:112811068-112811118	H1-hESC	embryonic stem cell:	embryo
49	chr2:112811068-112811118	HepG2	liver:	n/a
50	chr2:112811068-112811118	AG10803	skin:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:112640103..112643601-chr2:112810245..112815342,15	MCF-7	breast:
2	chr2:112654702..112658000-chr2:112810291..112813027,3	K562	blood:
3	chr2:112811018..112813475-chr2:113401964..113404333,2	K562	blood:
4	chr2:112665558..112667722-chr2:112810644..112812668,2	K562	blood:
5	chr2:112809505..112811729-chr2:113340407..113342286,2	MCF-7	breast:
6	chr2:112652127..112657107-chr2:112810449..112814378,4	K562	blood:
7	chr2:112804262..112806076-chr2:112808977..112811892,2	K562	blood:

No data

Variant related genes	Relation type
TMEM87B	TF binding region
TMEM87B	CpG island
ENSG00000125611	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000153208	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10169022	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10176660	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10176769	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10192728	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10194496	0.91[JPT][hapmap]
rs10195619	0.81[CEU][hapmap]
rs10207301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496439	0.81[JPT][hapmap]
rs10864895	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs1122970	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11673729	0.81[JPT][hapmap]
rs11674226	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11674883	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11674891	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11675946	0.81[JPT][hapmap]
rs11679125	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11679593	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11679801	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs11682629	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11683694	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11684321	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs11684476	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11685190	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11687451	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs11690440	0.82[ASN][1000 genomes]
rs11692445	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs11897014	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12995767	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13001162	0.89[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs13003919	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs13006203	0.81[JPT][hapmap]
rs13006228	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13020304	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs13024271	0.87[ASN][1000 genomes]
rs13027171	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs13033393	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs1554216	0.81[CEU][hapmap]
rs17174697	0.81[JPT][hapmap]
rs17779482	0.81[JPT][hapmap]
rs2271701	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs34128716	0.87[ASN][1000 genomes]
rs34240639	0.93[ASN][1000 genomes]
rs34593596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3761699	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs3811633	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs3811634	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4264571	0.81[JPT][hapmap]
rs4575728	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4632347	0.91[JPT][hapmap]
rs4848229	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4848238	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4848861	0.81[JPT][hapmap]
rs4848874	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4848971	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4848973	0.89[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4848975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4848979	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4848980	0.89[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6704665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736093	0.81[JPT][hapmap]
rs6743523	0.81[CEU][hapmap]
rs6748256	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs72829613	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7349221	0.81[JPT][hapmap]
rs7586558	0.87[ASN][1000 genomes]
rs7595212	0.81[JPT][hapmap]
rs7604403	0.81[JPT][hapmap]
rs870761	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs870763	0.82[CEU][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats 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
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv1793068	chr2:112784234-112816694	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6722814	RANBP2	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112803200-112811200	Weak transcription	Fetal Stomach	stomach
2	chr2:112804600-112811200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:112805600-112811200	Weak transcription	Adipose Nuclei	Adipose
4	chr2:112805600-112811200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:112805600-112811400	Weak transcription	Right Ventricle	heart
6	chr2:112805600-112811600	Weak transcription	Aorta	Aorta
7	chr2:112805600-112811600	Weak transcription	Gastric	stomach
8	chr2:112806000-112811400	Weak transcription	Right Atrium	heart
9	chr2:112806200-112811200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:112806400-112811200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:112806400-112811200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:112806400-112811200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:112807600-112811400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:112807600-112811600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:112807800-112811200	Weak transcription	Colonic Mucosa	Colon
16	chr2:112808200-112811200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:112808600-112811200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:112808600-112811200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:112809400-112811600	Weak transcription	Pancreas	Pancrea
20	chr2:112810000-112811800	Weak transcription	Small Intestine	intestine
21	chr2:112810400-112811400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:112810600-112811400	Enhancers	Fetal Intestine Small	intestine
23	chr2:112810800-112811200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:112810800-112811200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr2:112810800-112811200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:112810800-112811200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:112810800-112811400	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:112810800-112811400	Enhancers	Fetal Intestine Large	intestine
29	chr2:112810800-112811400	Flanking Active TSS	HepG2	liver
30	chr2:112811000-112811200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr2:112811000-112811200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:112811000-112811200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr2:112811000-112811200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:112811000-112811200	Enhancers	Primary T cells from cord blood	blood
35	chr2:112811000-112811200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr2:112811000-112811200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr2:112811000-112811200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:112811000-112811200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:112811000-112811200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr2:112811000-112811200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:112811000-112811200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:112811000-112811200	Enhancers	Brain Angular Gyrus	brain
43	chr2:112811000-112811200	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:112811000-112811200	Enhancers	Brain Hippocampus Middle	brain
45	chr2:112811000-112811200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:112811000-112811200	Enhancers	Brain Substantia Nigra	brain
47	chr2:112811000-112811200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr2:112811000-112811200	Enhancers	Fetal Heart	heart
49	chr2:112811000-112811200	Enhancers	Fetal Lung	lung
50	chr2:112811000-112811200	Enhancers	Rectal Mucosa Donor 31	rectum

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