Variant report

Variant	rs10516189
Chromosome Location	chr4:7783286-7783287
allele	A/G
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	RCOR1	chr4:7783095-7783403	K562	blood:	n/a	n/a
2	POLR2A	chr4:7782984-7783484	H1-neurons	neurons:	n/a	n/a
3	ATF1	chr4:7783122-7783478	K562	blood:	n/a	n/a
4	EP300	chr4:7783088-7783433	K562	blood:	n/a	n/a
5	JUND	chr4:7783209-7783409	K562	blood:	n/a	n/a
6	MYC	chr4:7783205-7783522	HUVEC	blood vessel:	n/a	n/a
7	UBTF	chr4:7783162-7783378	K562	blood:	n/a	n/a
8	ELF1	chr4:7783179-7783539	K562	blood:	n/a	chr4:7783339-7783352
9	POLR2A	chr4:7783023-7783460	H1-neurons	neurons:	n/a	n/a
10	JUN	chr4:7783160-7783640	HUVEC	blood vessel:	n/a	n/a
11	RUNX3	chr4:7783117-7783685	GM12878	blood:	n/a	chr4:7783371-7783380 chr4:7783371-7783380
12	POLR2A	chr4:7782915-7783682	PANC-1	pancreas:	n/a	n/a
13	TBL1XR1	chr4:7783275-7783358	K562	blood:	n/a	n/a
14	POLR2A	chr4:7783044-7783489	HUVEC	blood vessel:	n/a	n/a
15	ZMIZ1	chr4:7783238-7783392	K562	blood:	n/a	n/a
16	RUNX3	chr4:7783140-7783494	GM12878	blood:	n/a	chr4:7783371-7783380 chr4:7783371-7783380
17	POLR2A	chr4:7783048-7783378	K562	blood:	n/a	n/a
18	POLR2A	chr4:7783231-7783547	HUVEC	blood vessel:	n/a	n/a
19	GABPA	chr4:7783217-7783465	K562	blood:	n/a	n/a
20	POLR2A	chr4:7783161-7783515	SK-N-SH	brain:	n/a	n/a
21	GABPA	chr4:7783168-7783407	K562	blood:	n/a	n/a
22	EGR1	chr4:7783131-7783400	K562	blood:	n/a	n/a
23	EGR1	chr4:7783053-7783595	K562	blood:	n/a	chr4:7783519-7783541
24	POLR2A	chr4:7782901-7784056	K562	blood:	n/a	n/a
25	POLR2A	chr4:7783140-7783468	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr4:7783115-7783565	HUVEC	blood vessel:	n/a	n/a
27	FOS	chr4:7783107-7783543	HUVEC	blood vessel:	n/a	n/a
28	GATA2	chr4:7783079-7783528	HUVEC	blood vessel:	n/a	n/a
29	MAX	chr4:7783166-7783354	K562	blood:	n/a	n/a
30	POLR2A	chr4:7782955-7783752	HUVEC	blood vessel:	n/a	n/a
31	ELF1	chr4:7783116-7783517	K562	blood:	n/a	chr4:7783339-7783352

No.	Distal block	Cell Line	Cell type
1	chr4:7782182..7784812-chr4:7794360..7796536,2	K562	blood:
2	chr4:7765704..7768382-chr4:7782855..7784797,2	K562	blood:
3	chr4:7783261..7784863-chr4:7786642..7789248,2	K562	blood:

Variant related genes	Relation type
AFAP1	TF binding region
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11723068	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724590	0.85[CHB][hapmap]
rs11725132	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11725213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11728415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11731614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736326	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11736912	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11737451	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16841112	0.89[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs16841187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16841215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017177	0.93[AMR][1000 genomes]
rs2240053	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs2240054	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs2240055	0.93[AMR][1000 genomes]
rs2269849	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2269878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276967	0.87[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2285766	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2285767	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2285769	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2285770	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2285771	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs2285772	0.85[ASN][1000 genomes]
rs28604598	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4538480	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4689162	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4689164	0.84[GIH][hapmap]
rs4689165	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4689862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689863	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4997103	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55677626	0.91[AMR][1000 genomes]
rs55752670	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55817815	0.86[AMR][1000 genomes]
rs58790280	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58957020	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67476190	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67725344	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6852934	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs757252	0.93[AMR][1000 genomes]
rs7660919	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7695250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10516189	AICDA	trans	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
2	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
3	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
6	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:7773600-7783600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:7773800-7783400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:7774000-7783400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:7774600-7783400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:7775400-7783400	Weak transcription	Small Intestine	intestine
12	chr4:7776000-7784400	Strong transcription	Fetal Intestine Small	intestine
13	chr4:7776400-7787200	Weak transcription	Fetal Brain Male	brain
14	chr4:7776400-7790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:7776600-7785400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:7777000-7783600	Strong transcription	HMEC	breast
20	chr4:7777000-7785800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:7777200-7783400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:7777400-7784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:7778000-7784400	Strong transcription	Fetal Brain Female	brain
24	chr4:7779200-7783600	Strong transcription	Brain Germinal Matrix	brain
25	chr4:7780200-7783400	Weak transcription	Aorta	Aorta
26	chr4:7780200-7794400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:7780400-7784200	Genic enhancers	Fetal Muscle Leg	muscle
28	chr4:7780600-7785800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:7780600-7788000	Genic enhancers	Osteobl	bone
30	chr4:7780600-7800200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:7780800-7784800	Genic enhancers	NH-A	brain
32	chr4:7780800-7790600	Weak transcription	Pancreas	Pancrea
33	chr4:7781000-7783800	Weak transcription	NHEK	skin
34	chr4:7781000-7784400	Genic enhancers	Fetal Stomach	stomach
35	chr4:7781000-7800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:7781200-7783600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:7781200-7784000	Enhancers	Ovary	ovary
38	chr4:7781200-7796000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:7781400-7784000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:7781400-7784200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:7781400-7784800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:7781400-7786000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
45	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
46	chr4:7781600-7783800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:7781600-7784000	Enhancers	Spleen	Spleen
48	chr4:7781600-7784600	Weak transcription	A549	lung
49	chr4:7781600-7786000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr4:7781600-7786800	Weak transcription	Brain Cingulate Gyrus	brain

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