Variant report

Variant	rs7647531
Chromosome Location	chr3:105085111-105085112
allele	A/C
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	POLR2A	chr3:105085026-105088883	GM12892	blood:	n/a	n/a
2	TEAD4	chr3:105085067-105085877	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr3:105085100-105085250	Hela-S3	cervix:	n/a	n/a
4	JUND	chr3:105084988-105085903	A549	lung:	n/a	chr3:105085314-105085322 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
5	ELF1	chr3:105085007-105086714	GM12878	blood:	n/a	n/a
6	FOS	chr3:105084803-105085638	MCF10A-Er-Src	breast:	n/a	chr3:105085314-105085322 chr3:105085312-105085323 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
7	CBX3	chr3:105084925-105086039	HCT-116	colon:	n/a	n/a
8	SIN3AK20	chr3:105084834-105086152	MCF-7	breast:	n/a	n/a
9	NR3C1	chr3:105084962-105085849	A549	lung:	n/a	n/a
10	CTCF	chr3:105085020-105085170	NHLF	lung:	n/a	n/a
11	PBX3	chr3:105084919-105085944	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr3:105085003-105086355	HEK293	kidney:	n/a	n/a
13	USF1	chr3:105085009-105085464	A549	lung:	n/a	n/a
14	POLR2A	chr3:105084812-105086180	HCT-116	colon:	n/a	n/a
15	SIN3AK20	chr3:105084561-105086326	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:105084872-105086371	Gliobla	brain:	n/a	n/a
17	YY1	chr3:105085084-105085783	SK-N-SH_RA	brain:	n/a	chr3:105085243-105085254 chr3:105085505-105085519
18	POLR2A	chr3:105085099-105088820	GM12892	blood:	n/a	n/a
19	GATA3	chr3:105084629-105086038	A549	lung:	n/a	chr3:105085402-105085412 chr3:105085186-105085196 chr3:105085312-105085321
20	CHD2	chr3:105084939-105086257	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:105084905-105086791	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:105085074-105085456	SK-N-SH	brain:	n/a	n/a
23	BACH1	chr3:105084763-105086335	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:105084967-105085923	A549	lung:	n/a	n/a
25	FOSL2	chr3:105084501-105085876	A549	lung:	n/a	chr3:105085314-105085322 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
26	STAT3	chr3:105084630-105085253	MCF10A-Er-Src	breast:	n/a	chr3:105085241-105085253 chr3:105084756-105084776
27	RAD21	chr3:105084450-105086202	A549	lung:	n/a	chr3:105085505-105085515
28	MYC	chr3:105084236-105085998	A549	lung:	n/a	chr3:105085313-105085322 chr3:105085558-105085565
29	GATA3	chr3:105084642-105085931	SK-N-SH	brain:	n/a	chr3:105085402-105085412 chr3:105085186-105085196 chr3:105085312-105085321
30	FOXA2	chr3:105084832-105085510	A549	lung:	n/a	n/a
31	RAD21	chr3:105084234-105085870	SK-N-SH_RA	brain:	n/a	chr3:105085505-105085515
32	STAT3	chr3:105084683-105085691	MCF10A-Er-Src	breast:	n/a	chr3:105085241-105085253 chr3:105084756-105084776
33	POLR2A	chr3:105084469-105089450	MCF10A-Er-Src	breast:	n/a	n/a
34	EP300	chr3:105084774-105085891	A549	lung:	n/a	chr3:105085170-105085179 chr3:105085499-105085515
35	SP1	chr3:105085080-105085728	H1-hESC	embryonic stem cell:	n/a	chr3:105085504-105085518 chr3:105085508-105085517 chr3:105085507-105085519 chr3:105085477-105085498 chr3:105085509-105085518 chr3:105085507-105085519
36	SMARCC1	chr3:105084954-105087287	Hela-S3	cervix:	n/a	n/a
37	CEBPB	chr3:105084537-105085593	A549	lung:	n/a	n/a
38	FOS	chr3:105085075-105085742	MCF10A-Er-Src	breast:	n/a	chr3:105085314-105085322 chr3:105085312-105085323 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
39	E2F6	chr3:105085103-105085809	A549	lung:	n/a	n/a
40	MAX	chr3:105084399-105089068	A549	lung:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
41	TAF1	chr3:105084920-105086133	ECC-1	luminal epithelium:	n/a	n/a
42	MAX	chr3:105084981-105085946	H1-hESC	embryonic stem cell:	n/a	chr3:105085313-105085322 chr3:105085558-105085565
43	HA-E2F1	chr3:105084461-105086434	MCF-7	breast:	n/a	n/a
44	POLR2A	chr3:105084982-105088897	Hela-S3	cervix:	n/a	n/a
45	MTA3	chr3:105084867-105088990	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:105084936-105088887	GM19193	blood:	n/a	n/a
47	POLR2A	chr3:105085081-105089049	GM12878	blood:	n/a	n/a
48	MAX	chr3:105084930-105087138	ECC-1	luminal epithelium:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
49	MYBL2	chr3:105084963-105085907	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:105084996-105089016	GM18505	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:105085073-105085123	HCM	heart:	n/a
2	chr3:105085073-105085123	PrEC	prostate:	n/a
3	chr3:105085073-105085123	SK-N-SH_RA	brain:	n/a
4	chr3:105085073-105085123	HRCEpiC	kidney:	n/a
5	chr3:105085073-105085123	AG09309	skin:	n/a
6	chr3:105085073-105085123	HPAEpiC	pulmonary alveolar:	n/a
7	chr3:105085073-105085123	AG09319	gingival:	n/a
8	chr3:105085073-105085123	ovcar-3	ovarian:	n/a
9	chr3:105085073-105085123	HRE	kidney:	n/a
10	chr3:105085073-105085123	SK-N-MC	brain:	n/a
11	chr3:105085073-105085123	SKMC	muscle:	n/a
12	chr3:105085073-105085123	HL-60	blood:	n/a
13	chr3:105085073-105085123	HCF	heart:	n/a
14	chr3:105085073-105085123	BJ	skin:	n/a
15	chr3:105085073-105085123	CMK	blood:	n/a
16	chr3:105085073-105085123	HNPCEpiC	eye:	n/a
17	chr3:105085073-105085123	NB4	blood:	n/a
18	chr3:105085073-105085123	Caco-2	colon:	n/a
19	chr3:105085073-105085123	Jurkat	blood:	n/a
20	chr3:105085073-105085123	RPTEC	kidney:	n/a
21	chr3:105085073-105085123	AoSMC	blood vessel:	n/a
22	chr3:105085073-105085123	HUVEC	blood vessel:	n/a
23	chr3:105085073-105085123	HAEpiC	amniotic membrane:	n/a
24	chr3:105085073-105085123	HEEpiC	esophagus:	n/a
25	chr3:105085073-105085123	GM19239	blood:	n/a
26	chr3:105085073-105085123	GM12891	blood:	n/a
27	chr3:105085073-105085123	LNCaP	prostate:	n/a
28	chr3:105085073-105085123	NT2-D1	testis:	n/a
29	chr3:105085073-105085123	NHBE	bronchial:	n/a
30	chr3:105085073-105085123	AG04450	lung:	fetal
31	chr3:105085073-105085123	PANC-1	pancreas:	n/a
32	chr3:105085073-105085123	NH-A	brain:	n/a
33	chr3:105085073-105085123	H1-hESC	embryonic stem cell:	embryo
34	chr3:105085073-105085123	HRPEpiC	eye:	n/a
35	chr3:105085073-105085123	SK-N-SH	brain:	n/a
36	chr3:105085073-105085123	BE2_C	brain:	n/a
37	chr3:105085073-105085123	HCT-116	colon:	n/a
38	chr3:105085073-105085123	MCF10A-Er-Src	breast:	n/a
39	chr3:105085073-105085123	AG04449	skin:	fetal
40	chr3:105085073-105085123	ECC-1	luminal epithelium:	n/a
41	chr3:105085073-105085123	PFSK-1	brain:	n/a
42	chr3:105085073-105085123	MCF-7	breast:	n/a
43	chr3:105085073-105085123	IMR90	lung:	fetal
44	chr3:105085073-105085123	ProgFib	skin:	n/a
45	chr3:105085073-105085123	A549	lung:	n/a
46	chr3:105085073-105085123	HMEC	breast:	n/a
47	chr3:105085073-105085123	GM06990	blood:	n/a
48	chr3:105085073-105085123	U87	brain:	n/a
49	chr3:105085073-105085123	Hepatocyte	liver:	n/a
50	chr3:105085073-105085123	HepG2	liver:	n/a

Variant related genes	Relation type
ALCAM	TF binding region
ALCAM	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11710166	0.87[ASN][1000 genomes]
rs11710857	0.84[ASN][1000 genomes]
rs11714275	0.87[ASN][1000 genomes]
rs11714277	0.90[ASN][1000 genomes]
rs11716035	0.90[ASN][1000 genomes]
rs11718405	0.90[ASN][1000 genomes]
rs11718457	0.90[ASN][1000 genomes]
rs11719817	0.90[ASN][1000 genomes]
rs1898655	0.87[ASN][1000 genomes]
rs1955135	0.87[ASN][1000 genomes]
rs2895300	0.90[ASN][1000 genomes]
rs34029528	0.90[ASN][1000 genomes]
rs59322590	0.87[ASN][1000 genomes]
rs61522255	0.87[ASN][1000 genomes]
rs6771935	0.90[ASN][1000 genomes]
rs6771987	0.90[ASN][1000 genomes]
rs6786815	0.90[ASN][1000 genomes]
rs6794273	0.87[ASN][1000 genomes]
rs73177459	0.82[ASN][1000 genomes]
rs73177465	0.90[ASN][1000 genomes]
rs73177470	0.90[ASN][1000 genomes]
rs73177478	0.90[ASN][1000 genomes]
rs73177489	0.90[ASN][1000 genomes]
rs73177494	0.90[ASN][1000 genomes]
rs73179378	0.90[ASN][1000 genomes]
rs73179384	0.90[ASN][1000 genomes]
rs73181374	0.90[ASN][1000 genomes]
rs73181376	0.90[ASN][1000 genomes]
rs73181380	0.90[ASN][1000 genomes]
rs73181387	0.90[ASN][1000 genomes]
rs73181395	0.90[ASN][1000 genomes]
rs73181396	0.90[ASN][1000 genomes]
rs73181397	0.90[ASN][1000 genomes]
rs73181401	0.90[ASN][1000 genomes]
rs73183103	0.90[ASN][1000 genomes]
rs73183108	0.87[ASN][1000 genomes]
rs73183112	0.87[ASN][1000 genomes]
rs73183114	0.87[ASN][1000 genomes]
rs73183115	0.87[ASN][1000 genomes]
rs73183185	0.87[ASN][1000 genomes]
rs73183186	0.87[ASN][1000 genomes]
rs73183187	0.87[ASN][1000 genomes]
rs73183188	0.87[ASN][1000 genomes]
rs73183198	0.87[ASN][1000 genomes]
rs73185114	0.87[ASN][1000 genomes]
rs73185115	0.87[ASN][1000 genomes]
rs7647426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105083600-105086400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:105083800-105087800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:105083800-105088800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:105083800-105088800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:105084000-105085200	Flanking Active TSS	HUVEC	blood vessel
6	chr3:105084000-105085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:105084000-105086200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:105084000-105087600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:105084000-105088800	Active TSS	Brain Substantia Nigra	brain
10	chr3:105084000-105089000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:105084000-105089000	Active TSS	A549	lung
12	chr3:105084000-105089600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:105084200-105085400	Flanking Active TSS	HepG2	liver
14	chr3:105084200-105085800	Active TSS	Stomach Smooth Muscle	stomach
15	chr3:105084200-105087800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:105084200-105088400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:105084200-105089000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:105084200-105089000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:105084200-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:105084200-105089200	Active TSS	NHDF-Ad	bronchial
21	chr3:105084200-105089600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:105084200-105089600	Active TSS	NHLF	lung
23	chr3:105084200-105090400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:105084400-105085200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
25	chr3:105084400-105085400	Flanking Active TSS	Liver	Liver
26	chr3:105084400-105085400	Flanking Active TSS	Colonic Mucosa	Colon
27	chr3:105084400-105085800	Bivalent/Poised TSS	Psoas Muscle	Psoas
28	chr3:105084400-105086000	Active TSS	Pancreas	Pancrea
29	chr3:105084400-105086000	Active TSS	Right Atrium	heart
30	chr3:105084400-105086200	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr3:105084400-105086200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:105084400-105086200	Active TSS	Colon Smooth Muscle	Colon
33	chr3:105084400-105086400	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:105084400-105086400	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr3:105084400-105086600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr3:105084400-105087200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr3:105084400-105087800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:105084400-105088800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:105084400-105088800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:105084400-105088800	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:105084400-105088800	Active TSS	Gastric	stomach
42	chr3:105084400-105089000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:105084400-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:105084400-105089000	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr3:105084400-105089000	Active TSS	Aorta	Aorta
46	chr3:105084400-105089000	Active TSS	Brain Angular Gyrus	brain
47	chr3:105084400-105089000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:105084400-105089000	Active TSS	Ovary	ovary
49	chr3:105084400-105089400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:105084400-105089400	Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links