Variant report

Variant	rs6706397
Chromosome Location	chr2:181971800-181971801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr2:181971387-181972092	GM12878	blood:	n/a	n/a
2	ZNF384	chr2:181971607-181971804	GM12878	blood:	n/a	n/a
3	MEF2A	chr2:181971444-181972021	GM12878	blood:	n/a	chr2:181971740-181971748 chr2:181971730-181971745
4	PAX5	chr2:181971572-181971846	GM12878	blood:	n/a	n/a
5	FOS	chr2:181971531-181972054	HUVEC	blood vessel:	n/a	chr2:181971739-181971749 chr2:181971740-181971749 chr2:181971739-181971749 chr2:181971738-181971749 chr2:181971739-181971749 chr2:181971739-181971749
6	TCF3	chr2:181971447-181971907	GM12878	blood:	n/a	n/a
7	MTA3	chr2:181971376-181972092	GM12878	blood:	n/a	n/a
8	IRF4	chr2:181971396-181972017	GM12878	blood:	n/a	n/a
9	MYC	chr2:181971556-181971915	NB4	blood:	n/a	chr2:181971739-181971748
10	E2F4	chr2:181971764-181971994	MCF10A-Er-Src	breast:	n/a	n/a
11	SP1	chr2:181971382-181972084	A549	lung:	n/a	n/a
12	SMC3	chr2:181971605-181971882	Hela-S3	cervix:	n/a	n/a
13	NFATC1	chr2:181971355-181972053	GM12878	blood:	n/a	n/a
14	GABPA	chr2:181971523-181971910	A549	lung:	n/a	n/a
15	POU2F2	chr2:181971456-181972008	GM12891	blood:	n/a	n/a
16	KAP1	chr2:181971532-181971897	U2OS	brain:	n/a	n/a
17	EP300	chr2:181971457-181972044	A549	lung:	n/a	chr2:181971739-181971748
18	MAX	chr2:181971437-181972115	HCT-116	colon:	n/a	chr2:181971739-181971748
19	POU2F2	chr2:181971513-181971865	GM12878	blood:	n/a	n/a
20	BATF	chr2:181971450-181972019	GM12878	blood:	n/a	chr2:181971737-181971747 chr2:181971736-181971747
21	PAX5	chr2:181971517-181971924	GM12891	blood:	n/a	n/a
22	IKZF1	chr2:181971466-181972016	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:181971491-181972055	GM12892	blood:	n/a	n/a
24	RAD21	chr2:181971474-181971921	GM12878	blood:	n/a	n/a
25	TCF12	chr2:181971461-181972288	SK-N-SH	brain:	n/a	chr2:181972014-181972022
26	SIN3AK20	chr2:181971467-181972043	HCT-116	colon:	n/a	n/a
27	EP300	chr2:181971591-181971870	Hela-S3	cervix:	n/a	chr2:181971739-181971748
28	EP300	chr2:181971532-181971897	GM12878	blood:	n/a	chr2:181971739-181971748
29	MAX	chr2:181971459-181972094	A549	lung:	n/a	chr2:181971739-181971748
30	FOXM1	chr2:181971304-181972169	GM12878	blood:	n/a	n/a
31	JUND	chr2:181971458-181972125	HCT-116	colon:	n/a	chr2:181971739-181971749 chr2:181971740-181971749 chr2:181971739-181971749 chr2:181971739-181971749 chr2:181971739-181971749
32	CBX3	chr2:181971432-181972162	HCT-116	colon:	n/a	chr2:181971894-181971905
33	ELK1	chr2:181971631-181971910	GM12878	blood:	n/a	n/a
34	FOXM1	chr2:181971374-181972195	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:181971452-181972069	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr2:181971599-181971954	GM12878	blood:	n/a	chr2:181971739-181971748
37	RAD21	chr2:181971475-181972129	HCT-116	colon:	n/a	n/a
38	MAX	chr2:181971587-181971957	SK-N-SH	brain:	n/a	chr2:181971739-181971748
39	POLR2A	chr2:181971508-181971918	HCT-116	colon:	n/a	n/a
40	MXI1	chr2:181971531-181971924	GM12878	blood:	n/a	n/a
41	GATA3	chr2:181971453-181972153	A549	lung:	n/a	n/a
42	RXRA	chr2:181971548-181971955	GM12878	blood:	n/a	chr2:181971682-181971695 chr2:181971739-181971748 chr2:181971680-181971696 chr2:181971682-181971695 chr2:181971678-181971698 chr2:181971682-181971695
43	NFIC	chr2:181971240-181972391	GM12878	blood:	n/a	n/a
44	TCF12	chr2:181970724-181972162	SK-N-SH	brain:	n/a	chr2:181972014-181972022
45	BCLAF1	chr2:181971421-181972063	GM12878	blood:	n/a	chr2:181971739-181971748
46	JUND	chr2:181971616-181971869	K562	blood:	n/a	chr2:181971739-181971749 chr2:181971740-181971749 chr2:181971739-181971749 chr2:181971739-181971749 chr2:181971739-181971749
47	POLR2A	chr2:181971518-181971870	GM12891	blood:	n/a	n/a
48	CEBPB	chr2:181971558-181971933	GM12878	blood:	n/a	n/a
49	GATA3	chr2:181970750-181972231	SK-N-SH	brain:	n/a	n/a
50	TBP	chr2:181971493-181971912	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:181839506..181842433-chr2:181971642..181974430,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBE2E3-4	chr2:181971351-181972525	ucscGeneNc_uc002uns_1

Variant related genes	Relation type
ENSG00000238171	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11891215	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11893821	0.87[EUR][1000 genomes]
rs12999974	0.87[EUR][1000 genomes]
rs13011751	0.90[ASN][1000 genomes]
rs13012524	0.93[ASN][1000 genomes]
rs13020845	0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs13025711	0.84[EUR][1000 genomes]
rs13033467	0.87[EUR][1000 genomes]
rs34601234	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34714467	0.87[EUR][1000 genomes]
rs35049898	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35323141	0.86[EUR][1000 genomes]
rs35543145	0.87[EUR][1000 genomes]
rs4366861	0.86[MEX][hapmap]
rs4595925	0.86[MEX][hapmap]
rs4667005	0.86[MEX][hapmap]
rs55664819	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55900432	0.87[EUR][1000 genomes]
rs55954384	0.87[EUR][1000 genomes]
rs56169464	0.84[EUR][1000 genomes]
rs59395276	0.84[EUR][1000 genomes]
rs62178846	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433892	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6433895	0.84[EUR][1000 genomes]
rs6706696	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6710650	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6711938	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6744130	0.86[MEX][hapmap]
rs6746347	0.87[EUR][1000 genomes]
rs6759865	0.87[EUR][1000 genomes]
rs7558428	0.87[EUR][1000 genomes]
rs7559803	0.86[MEX][hapmap]
rs7566146	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7566256	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7566434	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7569991	0.80[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7580796	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7592486	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7598960	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431824	chr2:181946115-182118559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:181969000-181972400	Enhancers	Dnd41	blood
2	chr2:181969000-181974600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:181969200-181972000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:181969200-181972400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:181969200-181972600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:181969200-181973200	Enhancers	Primary T cells from cord blood	blood
7	chr2:181969200-181973200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr2:181969200-181973600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:181969200-181974200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:181969400-181971800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr2:181969400-181972400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr2:181969400-181972600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:181969400-181972600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:181969400-181972600	Enhancers	HSMMtube	muscle
15	chr2:181969400-181972800	Enhancers	Fetal Brain Male	brain
16	chr2:181969400-181973400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:181969400-181974000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr2:181969400-181974200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:181969600-181971800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:181969600-181971800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:181969600-181972400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:181969600-181972400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:181969600-181972400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:181969600-181972400	Enhancers	Osteobl	bone
25	chr2:181969600-181973200	Enhancers	NHDF-Ad	bronchial
26	chr2:181969800-181972400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:181969800-181972400	Enhancers	HSMM	muscle
28	chr2:181970000-181972200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:181970200-181972400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:181970200-181972400	Enhancers	Hela-S3	cervix
31	chr2:181970200-181972400	Enhancers	HMEC	breast
32	chr2:181970200-181972400	Enhancers	NHEK	skin
33	chr2:181970200-181973200	Enhancers	NHLF	lung
34	chr2:181970400-181972200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:181970400-181972200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:181970400-181972400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:181970600-181972000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:181970600-181972000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:181970800-181971800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:181970800-181972000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr2:181970800-181972000	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:181970800-181972400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:181970800-181972400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr2:181970800-181974000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:181971000-181971800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr2:181971000-181971800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:181971000-181971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:181971000-181972000	Enhancers	Thymus	Thymus
49	chr2:181971000-181972200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr2:181971000-181972200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links