Variant report

Variant	rs7415820
Chromosome Location	chr1:113169449-113169450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113169335-113169856	U87	brain:	n/a	n/a
2	POLR2A	chr1:113169335-113169924	U87	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113160312..113164959-chr1:113166253..113170624,10	MCF-7	breast:
2	chr1:113166891..113170892-chr1:113175321..113178466,4	MCF-7	breast:
3	chr1:113167367..113170030-chr1:113193685..113196891,3	K562	blood:
4	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
5	chr1:113166898..113170034-chr1:113215847..113218393,3	K562	blood:
6	chr1:113166898..113170034-chr1:113215847..113218530,3	K562	blood:
7	chr1:113167976..113172227-chr1:113246480..113250465,5	K562	blood:
8	chr1:113167944..113171007-chr1:113245720..113249508,3	MCF-7	breast:

No data

Variant related genes	Relation type
MRPL53P1	TF binding region
ENSG00000252750	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001494	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10745330	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs10776755	0.89[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs10776757	0.89[CEU][hapmap]
rs10857963	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs11102497	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11102512	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11584092	0.88[CEU][hapmap]
rs12046208	0.89[CEU][hapmap];0.83[GIH][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs12046329	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12046466	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12126277	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12728001	0.96[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs1994604	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932532	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932536	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999154	0.88[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999155	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999157	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3013431	0.83[ASN][1000 genomes]
rs3013439	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3013440	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3103450	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351372	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs4838959	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs4839254	0.85[CEU][hapmap]
rs6537743	0.90[EUR][1000 genomes]
rs6537748	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs6537749	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs6666579	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6669096	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6682737	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691932	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700673	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7513716	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs7522288	0.82[CEU][hapmap]
rs7524494	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7544663	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes]
rs7546094	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554345	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554916	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs902289	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs910697	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs9429486	0.89[CEU][hapmap]
rs954679	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
6	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs7415820	WNT2B	cis	parietal	SCAN
rs7415820	ST7L	cis	Adipose Subcutaneous	GTEx
rs7415820	ST7L	cis	lung	GTEx
rs7415820	ST7L	cis	Lymphoblastoid	GTEx
rs7415820	ST7L	cis	Thyroid	GTEx
rs7415820	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs7415820	ST7L	cis	uninvolved skin	skin_eQTL
rs7415820	ST7L	cis	Esophagus Muscularis	GTEx
rs7415820	ST7L	cis	normal skin	skin_eQTL
rs7415820	ST7L	cis	multi-tissue	Pritchard
rs7415820	ST7L	cis	lesional skin	skin_eQTL
rs7415820	SYCP1	cis	parietal	SCAN
rs7415820	ALX3	cis	parietal	SCAN
rs7415820	ST7L	cis	lymphoblastoid	seeQTL
rs7415820	C1orf162	cis	parietal	SCAN
rs7415820	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs7415820	ST7L	cis	Heart Left Ventricle	GTEx
rs7415820	ST7L	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163400-113170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:113163600-113171600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:113163600-113173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:113163600-113180600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
6	chr1:113163800-113169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:113163800-113173200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:113163800-113176000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:113164000-113173200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:113164000-113190000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:113164200-113175800	Weak transcription	Fetal Brain Female	brain
14	chr1:113164200-113180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
16	chr1:113164600-113171400	Weak transcription	Placenta	Placenta
17	chr1:113164800-113179200	Weak transcription	Colonic Mucosa	Colon
18	chr1:113165200-113172200	Weak transcription	Brain Germinal Matrix	brain
19	chr1:113165400-113174400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:113165400-113175200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:113165400-113176400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:113165600-113174400	Genic enhancers	K562	blood
23	chr1:113166000-113173200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:113166600-113169800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:113167200-113169600	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr1:113167200-113169800	Strong transcription	Fetal Thymus	thymus
27	chr1:113167200-113169800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
28	chr1:113167400-113169600	Genic enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:113167400-113169800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:113167400-113173600	Genic enhancers	Monocytes-CD14+_RO01746	blood
31	chr1:113167600-113169600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
32	chr1:113167600-113169600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:113167600-113170000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:113167600-113170000	Genic enhancers	Dnd41	blood
35	chr1:113167600-113170200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:113167600-113170200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:113167800-113176200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr1:113168000-113169800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:113168000-113170200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:113168000-113171000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:113168000-113180000	Weak transcription	Aorta	Aorta
42	chr1:113168200-113170000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:113168200-113170000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr1:113168200-113171200	Weak transcription	Small Intestine	intestine
45	chr1:113168400-113169600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:113168400-113169600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:113168400-113169800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:113168400-113169800	Genic enhancers	HMEC	breast
49	chr1:113168400-113170000	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr1:113168400-113171000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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