Variant report

Variant	rs3806256
Chromosome Location	chr1:155035611-155035612
allele	C/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	MTA3	chr1:155035112-155036488	GM12878	blood:	n/a	n/a
2	STAT5A	chr1:155035166-155036528	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:155035483-155036515	HUVEC	blood vessel:	n/a	n/a
4	MAX	chr1:155035061-155036439	H1-hESC	embryonic stem cell:	n/a	chr1:155035674-155035683 chr1:155036030-155036040
5	POLR2A	chr1:155034884-155036490	HL-60	blood:	n/a	n/a
6	CTCF	chr1:155034984-155035742	HCT-116	colon:	n/a	chr1:155035307-155035325
7	TCF12	chr1:155035015-155037225	A549	lung:	n/a	n/a
8	POLR2A	chr1:155035111-155036559	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr1:155035527-155035884	GM19239	blood:	n/a	n/a
10	POLR2A	chr1:155035600-155036834	HepG2	liver:	n/a	n/a
11	CTCF	chr1:155034931-155035880	GM19240	blood:	n/a	chr1:155035307-155035325
12	MAX	chr1:155034981-155036588	A549	lung:	n/a	chr1:155035674-155035683 chr1:155036030-155036040 chr1:155036550-155036560
13	BCL3	chr1:155035137-155036478	A549	lung:	n/a	chr1:155035589-155035598 chr1:155035586-155035595 chr1:155035536-155035545
14	RCOR1	chr1:155035261-155035768	K562	blood:	n/a	n/a
15	RAD21	chr1:155034984-155036525	HCT-116	colon:	n/a	n/a
16	MAX	chr1:155035063-155035879	A549	lung:	n/a	chr1:155035674-155035683
17	MAX	chr1:155034905-155035883	H1-hESC	embryonic stem cell:	n/a	chr1:155035674-155035683
18	JUND	chr1:155035215-155035916	A549	lung:	n/a	chr1:155035534-155035543
19	POLR2A	chr1:155035097-155036994	K562	blood:	n/a	n/a
20	MAX	chr1:155035108-155036491	MCF-7	breast:	n/a	chr1:155035674-155035683 chr1:155036030-155036040
21	POLR2A	chr1:155035486-155035631	A549	lung:	n/a	n/a
22	CHD1	chr1:155035015-155037233	IMR90	lung:	n/a	chr1:155036566-155036576 chr1:155036559-155036569 chr1:155036552-155036562
23	POLR2A	chr1:155035516-155036437	Hela-S3	cervix:	n/a	n/a
24	SMC3	chr1:155035127-155035803	K562	blood:	n/a	n/a
25	CTCF	chr1:155035132-155035885	GM19238	blood:	n/a	chr1:155035307-155035325
26	RAD21	chr1:155034977-155036565	HCT-116	colon:	n/a	n/a
27	MAZ	chr1:155035158-155036975	GM12878	blood:	n/a	chr1:155035674-155035683 chr1:155036030-155036040 chr1:155036772-155036782 chr1:155036550-155036560
28	ZNF263	chr1:155035362-155037098	HEK293-T-REx	kidney:	n/a	chr1:155035577-155035586
29	POLR2A	chr1:155035527-155035773	HUVEC	blood vessel:	n/a	n/a
30	SIN3A	chr1:155034825-155037086	H1-hESC	embryonic stem cell:	n/a	chr1:155036742-155036751 chr1:155035584-155035595
31	CTCF	chr1:155034734-155036449	HCT-116	colon:	n/a	chr1:155035307-155035325
32	CTCF	chr1:155035054-155035660	K562	blood:	n/a	chr1:155035307-155035325
33	RAD21	chr1:155035041-155035633	MCF-7	breast:	n/a	n/a
34	CTCF	chr1:155034929-155036125	GM12878	blood:	n/a	chr1:155035307-155035325
35	RAD21	chr1:155035001-155035703	A549	lung:	n/a	n/a
36	CTCF	chr1:155033668-155036363	A549	lung:	n/a	chr1:155035307-155035325
37	MAX	chr1:155035507-155035756	K562	blood:	n/a	chr1:155035674-155035683
38	POLR2A	chr1:155035164-155035622	HCT-116	colon:	n/a	n/a
39	RCOR1	chr1:155035204-155037219	K562	blood:	n/a	n/a
40	TCF7L2	chr1:155035264-155037021	HCT-116	colon:	n/a	chr1:155035612-155035622
41	E2F6	chr1:155035361-155036430	K562	blood:	n/a	chr1:155035528-155035537 chr1:155035539-155035549 chr1:155035536-155035546 chr1:155036026-155036038
42	YY1	chr1:155035022-155035841	H1-hESC	embryonic stem cell:	n/a	chr1:155035584-155035593 chr1:155035587-155035598 chr1:155035590-155035599
43	SMC3	chr1:155035123-155036118	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:155035125-155035757	HCT-116	colon:	n/a	n/a
45	ELF1	chr1:155035027-155035873	GM12878	blood:	n/a	chr1:155035590-155035599 chr1:155035529-155035541 chr1:155035321-155035330
46	POLR2A	chr1:155035211-155035745	A549	lung:	n/a	n/a
47	MAZ	chr1:155035072-155035742	IMR90	lung:	n/a	chr1:155035674-155035683
48	POLR2A	chr1:155035562-155036595	PFSK-1	brain:	n/a	n/a
49	ELF1	chr1:155035546-155036554	MCF-7	breast:	n/a	chr1:155035590-155035599
50	E2F6	chr1:155035607-155035773	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154989698..154990221-chr1:155035321..155036093,2	K562	blood:
2	chr1:154944693..154948498-chr1:155033358..155037574,5	K562	blood:
3	chr1:154939878..154945720-chr1:155033369..155036154,5	MCF-7	breast:
4	chr1:155034862..155035730-chr1:155140353..155140934,2	MCF-7	breast:
5	chr1:155034878..155035737-chr1:155140076..155140955,5	K562	blood:
6	chr1:155034568..155037098-chr1:155106619..155109204,2	MCF-7	breast:
7	chr1:155034968..155037453-chr1:155166180..155167789,2	MCF-7	breast:
8	chr1:154971009..154978300-chr1:155033602..155036845,7	K562	blood:
9	chr1:155033872..155036303-chr1:155100815..155102776,3	MCF-7	breast:
10	chr1:154927481..154932587-chr1:155031885..155037682,6	MCF-7	breast:
11	chr1:154948517..154951842-chr1:155034906..155036770,3	MCF-7	breast:
12	chr1:154943492..154949367-chr1:155033837..155038035,9	MCF-7	breast:
13	chr1:155033847..155038699-chr1:155096296..155100742,10	MCF-7	breast:
14	chr1:154933177..154934907-chr1:155034094..155037723,3	MCF-7	breast:
15	chr1:154908789..154910425-chr1:155034251..155037160,2	K562	blood:
16	chr1:154932754..154935795-chr1:155033186..155037944,5	MCF-7	breast:
17	chr1:154934033..154936309-chr1:155035273..155037731,2	K562	blood:
18	chr1:154945666..154948498-chr1:155033358..155037574,4	K562	blood:
19	chr1:155034206..155036966-chr1:155163322..155165857,2	MCF-7	breast:
20	chr1:154969072..154977664-chr1:155030052..155039846,22	MCF-7	breast:
21	chr1:155034804..155037518-chr1:155055135..155058799,58	K562	blood:
22	chr1:154529028..154532359-chr1:155034427..155037689,4	MCF-7	breast:

Variant related genes	Relation type
EFNA3	TF binding region
ENSG00000251246	TF binding region
EFNA4	TF binding region
ENSG00000271380	Chromatin interaction
ENSG00000264349	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000163346	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000163348	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000231064	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000271748	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1001848	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10908454	0.85[JPT][hapmap]
rs10908455	0.85[JPT][hapmap]
rs10908456	0.85[JPT][hapmap]
rs11264304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11264306	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11264307	0.81[ASN][1000 genomes]
rs11264314	0.82[JPT][hapmap]
rs11264319	0.85[JPT][hapmap]
rs11264329	0.85[JPT][hapmap]
rs12040970	0.85[JPT][hapmap]
rs12047986	0.81[ASN][1000 genomes]
rs12145362	0.85[JPT][hapmap]
rs1462855	0.85[JPT][hapmap]
rs1564124	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1870939	0.85[JPT][hapmap]
rs2306124	0.85[JPT][hapmap]
rs2306125	0.86[JPT][hapmap]
rs35902694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3765087	0.85[JPT][hapmap]
rs3766916	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4045192	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845407	0.85[JPT][hapmap]
rs4845408	0.85[JPT][hapmap]
rs4845712	0.81[ASN][1000 genomes]
rs6427158	0.85[JPT][hapmap]
rs6665822	0.85[JPT][hapmap]
rs6693477	0.85[JPT][hapmap]
rs7365544	0.85[JPT][hapmap]
rs7367207	0.85[JPT][hapmap]
rs7367897	1.00[JPT][hapmap]
rs7368345	0.85[JPT][hapmap]
rs7534162	0.85[JPT][hapmap]
rs7548955	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv872456	chr1:155028692-155035611	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3806256	ETV3L	cis	parietal	SCAN
rs3806256	OTUD7B	cis	parietal	SCAN
rs3806256	TPM3	cis	parietal	SCAN
rs3806256	APOA1BP	cis	cerebellum	SCAN
rs3806256	INTS3	cis	cerebellum	SCAN
rs3806256	S100A9	cis	parietal	SCAN
rs3806256	UBE2Q1	cis	cerebellum	SCAN
rs3806256	SETDB1	cis	parietal	SCAN
rs3806256	ADAM15	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155031400-155035800	Weak transcription	HSMMtube	muscle
2	chr1:155031600-155035800	Weak transcription	Aorta	Aorta
3	chr1:155034000-155036800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:155034200-155035800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:155034200-155036200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:155034200-155037000	Bivalent Enhancer	Fetal Brain Male	brain
7	chr1:155034400-155035800	Weak transcription	Fetal Kidney	kidney
8	chr1:155034400-155035800	Weak transcription	HSMM	muscle
9	chr1:155034400-155036000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:155034400-155036200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:155034400-155036800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:155034600-155035800	Weak transcription	HUVEC	blood vessel
13	chr1:155034600-155036000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:155034600-155037200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr1:155034800-155036000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:155034800-155036200	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr1:155034800-155037000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr1:155035000-155035800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr1:155035000-155036000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:155035000-155036000	Weak transcription	Small Intestine	intestine
21	chr1:155035000-155036000	Flanking Active TSS	A549	lung
22	chr1:155035000-155036200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:155035000-155036200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:155035000-155036200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:155035000-155036200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:155035000-155036200	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr1:155035000-155036200	Flanking Active TSS	Pancreas	Pancrea
28	chr1:155035000-155036200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr1:155035000-155036200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr1:155035000-155037000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr1:155035000-155037200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:155035200-155035800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:155035200-155035800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr1:155035200-155036000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr1:155035200-155036000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr1:155035200-155036200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr1:155035200-155036200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr1:155035200-155036200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr1:155035200-155036200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:155035200-155036200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr1:155035200-155036200	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr1:155035200-155036200	Flanking Bivalent TSS/Enh	Thymus	Thymus
43	chr1:155035200-155037000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:155035200-155037000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:155035200-155037400	Flanking Active TSS	Colonic Mucosa	Colon
46	chr1:155035200-155037400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:155035200-155037600	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr1:155035200-155037600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:155035400-155035800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:155035400-155035800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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