Variant report

Variant	rs3812860
Chromosome Location	chr13:67804232-67804233
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	POLR2A	chr13:67804039-67805591	ECC-1	luminal epithelium:	n/a	n/a
2	MYC	chr13:67804148-67804246	K562	blood:	n/a	n/a
3	POLR2A	chr13:67804202-67804565	A549	lung:	n/a	n/a
4	CREB1	chr13:67804081-67805051	HepG2	liver:	n/a	n/a
5	POLR2A	chr13:67804102-67805562	HEK293	kidney:	n/a	n/a
6	SIN3A	chr13:67803668-67805659	H1-hESC	embryonic stem cell:	n/a	chr13:67804783-67804792
7	ZBTB33	chr13:67804229-67804542	A549	lung:	n/a	n/a
8	NFYB	chr13:67804016-67804992	GM12878	blood:	n/a	chr13:67804535-67804550 chr13:67804537-67804552 chr13:67804536-67804550 chr13:67804535-67804550
9	MAX	chr13:67804098-67805589	A549	lung:	n/a	n/a
10	CTBP2	chr13:67804180-67805479	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr13:67804078-67805490	A549	lung:	n/a	n/a
12	POLR2A	chr13:67804033-67805440	U87	brain:	n/a	n/a
13	REST	chr13:67804210-67804804	SK-N-SH	brain:	n/a	chr13:67804677-67804690 chr13:67804717-67804730
14	GATA2	chr13:67803222-67805671	SH-SY5Y	brain:	n/a	chr13:67803716-67803725 chr13:67803716-67803723 chr13:67805544-67805554 chr13:67803716-67803723 chr13:67803717-67803734 chr13:67803712-67803728 chr13:67803464-67803475 chr13:67803709-67803730 chr13:67803712-67803728 chr13:67803716-67803725 chr13:67803716-67803723 chr13:67803715-67803725
15	REST	chr13:67803603-67805800	H1-neurons	neurons:	n/a	chr13:67804677-67804690 chr13:67805223-67805243 chr13:67804717-67804730
16	POLR2A	chr13:67804033-67805418	U87	brain:	n/a	n/a
17	HA-E2F1	chr13:67803652-67805615	MCF-7	breast:	n/a	chr13:67804835-67804844 chr13:67804518-67804528 chr13:67804634-67804643 chr13:67804859-67804868 chr13:67804523-67804532
18	POLR2A	chr13:67804188-67805298	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP1	chr13:67804152-67804983	A549	lung:	n/a	chr13:67804521-67804533 chr13:67804524-67804537 chr13:67804522-67804532 chr13:67804523-67804532 chr13:67804521-67804533 chr13:67804522-67804532 chr13:67804582-67804593 chr13:67804528-67804549 chr13:67804522-67804531 chr13:67804522-67804531
20	MAX	chr13:67804081-67805406	NB4	blood:	n/a	n/a
21	POLR2A	chr13:67804092-67805001	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr13:67804035-67806032	MCF10A-Er-Src	breast:	n/a	n/a
23	TAF1	chr13:67804171-67805551	ECC-1	luminal epithelium:	n/a	n/a
24	SIN3AK20	chr13:67804099-67804538	H1-hESC	embryonic stem cell:	n/a	n/a
25	PBX3	chr13:67804203-67804662	A549	lung:	n/a	chr13:67804538-67804547
26	POLR2A	chr13:67804178-67805426	MCF-7	breast:	n/a	n/a
27	REST	chr13:67804069-67804697	A549	lung:	n/a	chr13:67804677-67804690
28	NFYB	chr13:67804226-67804786	K562	blood:	n/a	chr13:67804535-67804550 chr13:67804537-67804552 chr13:67804536-67804550 chr13:67804535-67804550
29	POLR2A	chr13:67804135-67805520	Gliobla	brain:	n/a	n/a
30	SIN3AK20	chr13:67803973-67804861	SK-N-SH	brain:	n/a	n/a
31	FOSL2	chr13:67804212-67804685	A549	lung:	n/a	chr13:67804656-67804670 chr13:67804537-67804546
32	CHD2	chr13:67804185-67805082	HepG2	liver:	n/a	chr13:67804632-67804642
33	SP1	chr13:67804160-67805263	A549	lung:	n/a	chr13:67804521-67804533 chr13:67804524-67804537 chr13:67804522-67804532 chr13:67804523-67804532 chr13:67804521-67804533 chr13:67804522-67804532 chr13:67804582-67804593 chr13:67804528-67804549 chr13:67804522-67804531 chr13:67804522-67804531
34	WRNIP1	chr13:67804124-67804514	GM12878	blood:	n/a	n/a
35	POLR2A	chr13:67803951-67805634	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr13:67804165-67805482	A549	lung:	n/a	n/a
37	POLR2A	chr13:67804164-67805574	H1-neurons	neurons:	n/a	n/a
38	MAX	chr13:67804031-67805610	SK-N-SH	brain:	n/a	n/a
39	TCF12	chr13:67803984-67805377	A549	lung:	n/a	n/a
40	SIN3AK20	chr13:67804192-67804745	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr13:67804216-67805436	MCF-7	breast:	n/a	n/a
42	TAF1	chr13:67803913-67805144	A549	lung:	n/a	n/a
43	POLR2A	chr13:67803688-67805072	PBDE	blood:	n/a	n/a
44	E2F4	chr13:67803714-67804776	MCF10A-Er-Src	breast:	n/a	chr13:67804518-67804528 chr13:67804634-67804643 chr13:67804523-67804532
45	POLR2A	chr13:67803973-67805672	U87	brain:	n/a	n/a
46	POLR2A	chr13:67804037-67805641	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr13:67803702-67805622	Raji	blood:	n/a	n/a
48	CHD1	chr13:67804226-67804354	GM12878	blood:	n/a	n/a
49	POLR2A	chr13:67804225-67805000	HUVEC	blood vessel:	n/a	n/a
50	JUND	chr13:67804168-67805193	H1-hESC	embryonic stem cell:	n/a	chr13:67804656-67804670 chr13:67804537-67804546

Variant related genes	Relation type
PCDH9	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12857493	0.84[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1325677	0.85[ASN][1000 genomes]
rs1325678	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925750	0.92[ASN][1000 genomes]
rs1983871	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1983949	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2147998	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2182229	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2325025	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2325027	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2985931	0.85[GIH][hapmap]
rs3812859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4097309	0.84[ASN][1000 genomes]
rs4884719	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs4884720	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs700329	0.88[ASN][1000 genomes]
rs71427643	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7489531	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7985679	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7992750	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8002263	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9317650	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs9317651	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9317655	0.85[ASN][1000 genomes]
rs9529199	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9529206	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9541034	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9541035	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9541039	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9541041	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9571740	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9571744	0.85[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	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr13:67795400-67805600	Active TSS	Brain Substantia Nigra	brain
2	chr13:67796200-67806000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr13:67796200-67806200	Active TSS	Brain Angular Gyrus	brain
4	chr13:67797200-67806000	Active TSS	Right Ventricle	heart
5	chr13:67797600-67806200	Active TSS	Fetal Kidney	kidney
6	chr13:67799800-67805800	Active TSS	Brain Anterior Caudate	brain
7	chr13:67799800-67805800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:67800200-67805600	Active TSS	Fetal Brain Female	brain
9	chr13:67800200-67806000	Active TSS	Left Ventricle	heart
10	chr13:67800400-67806000	Active TSS	Brain Hippocampus Middle	brain
11	chr13:67800800-67806600	Active TSS	Brain Cingulate Gyrus	brain
12	chr13:67801200-67810000	Active TSS	Right Atrium	heart
13	chr13:67801600-67808400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr13:67802000-67805200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
15	chr13:67802000-67806000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:67802000-67806200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:67802000-67806400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:67802200-67805600	Active TSS	Lung	lung
19	chr13:67802400-67804400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr13:67802400-67804600	Active TSS	Colonic Mucosa	Colon
21	chr13:67802400-67806000	Active TSS	Aorta	Aorta
22	chr13:67802400-67806000	Active TSS	Fetal Stomach	stomach
23	chr13:67802400-67809400	Active TSS	A549	lung
24	chr13:67802600-67804400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr13:67802600-67805200	Active TSS	Thymus	Thymus
26	chr13:67802600-67805800	Active TSS	Placenta Amnion	Placenta Amnion
27	chr13:67802600-67806000	Active TSS	HSMM	muscle
28	chr13:67802600-67806000	Active TSS	HSMMtube	muscle
29	chr13:67802800-67805800	Active TSS	Muscle Satellite Cultured Cells	--
30	chr13:67802800-67806000	Active TSS	Fetal Muscle Trunk	muscle
31	chr13:67802800-67806200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:67803000-67804400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr13:67803000-67804600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr13:67803000-67805400	Active TSS	Fetal Brain Male	brain
35	chr13:67803000-67805600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:67803000-67805600	Active TSS	Gastric	stomach
37	chr13:67803000-67805800	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr13:67803000-67806000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr13:67803000-67806000	Active TSS	Colon Smooth Muscle	Colon
40	chr13:67803000-67806000	Active TSS	Fetal Heart	heart
41	chr13:67803000-67806000	Active TSS	Psoas Muscle	Psoas
42	chr13:67803000-67806200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:67803000-67806200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr13:67803200-67804400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr13:67803200-67804400	Flanking Bivalent TSS/Enh	Liver	Liver
46	chr13:67803200-67805800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr13:67803200-67805800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:67803200-67805800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:67803200-67806000	Active TSS	NHDF-Ad	bronchial
50	chr13:67803200-67806800	Active TSS	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links