Variant report

Variant	rs6537747
Chromosome Location	chr1:113179597-113179598
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	KAP1	chr1:113179587-113180834	HEK293	kidney:	n/a	n/a
2	FOS	chr1:113179263-113179739	HUVEC	blood vessel:	n/a	chr1:113179459-113179470
3	FOS	chr1:113179318-113179600	MCF10A-Er-Src	breast:	n/a	chr1:113179459-113179470
4	TCF7L2	chr1:113179561-113180773	PANC-1	pancreas:	n/a	n/a
5	GATA3	chr1:113179126-113180643	SK-N-SH	brain:	n/a	chr1:113179348-113179359 chr1:113180258-113180266
6	GATA3	chr1:113179521-113180668	A549	lung:	n/a	chr1:113180258-113180266
7	PBX3	chr1:113179151-113179660	SK-N-SH	brain:	n/a	n/a
8	MAFK	chr1:113179301-113179697	K562	blood:	n/a	n/a
9	PBX3	chr1:113179155-113179741	SK-N-SH	brain:	n/a	n/a
10	MAFF	chr1:113179302-113179602	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113178814..113181751-chr1:113240600..113243553,2	MCF-7	breast:
2	chr1:113179573..113181376-chr1:113254549..113257540,2	K562	blood:
3	chr1:113178255..113183299-chr1:113188318..113192161,4	K562	blood:

Variant related genes	Relation type
RNU7-70P	TF binding region
ENSG00000155367	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10745332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857969	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102494	0.82[EUR][1000 genomes]
rs11102508	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102510	0.92[EUR][1000 genomes]
rs11102517	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118370	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12119489	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12125361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126494	0.83[EUR][1000 genomes]
rs12136781	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12137107	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12138335	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12143068	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1238	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12401734	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs12402469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12402929	1.00[CEU][hapmap]
rs12406906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12739994	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12750023	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12750621	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12758377	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17438324	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2932529	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2932534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932537	0.92[GIH][hapmap]
rs2932538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932539	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3013433	0.87[EUR][1000 genomes]
rs3013441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34531155	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35482634	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36029940	0.82[EUR][1000 genomes]
rs3762335	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[ASN][1000 genomes]
rs3790612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.88[ASN][1000 genomes]
rs3795820	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4240534	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838960	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838961	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61818772	0.82[EUR][1000 genomes]
rs61818800	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap]
rs6537742	0.84[CEU][hapmap]
rs6537744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6537745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658555	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs6659677	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6661642	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6663922	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668533	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs6671645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6672761	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6673930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674053	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674068	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6681371	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs6682678	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6690169	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690292	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691025	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691917	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693880	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6696991	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6698030	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6701351	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7415988	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7516421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7519368	0.85[EUR][1000 genomes]
rs7522110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7527076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7537789	0.88[ASN][1000 genomes]
rs7542820	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546203	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549547	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7552692	0.86[ASN][1000 genomes]
rs9429694	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9662162	0.83[ASN][1000 genomes]
rs999923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6537747	CTTNBP2NL	cis	parietal	SCAN
rs6537747	ST7L	cis	Lymphoblastoid	GTEx
rs6537747	HBXIP	cis	parietal	SCAN
rs6537747	ST7L	cis	Nerve Tibial	GTEx
rs6537747	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs6537747	ST7L	cis	lung	GTEx
rs6537747	ST7L	cis	multi-tissue	Pritchard
rs6537747	CAPZA1	cis	lymphoblastoid	seeQTL
rs6537747	ST7L	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163600-113180600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
3	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:113164000-113190000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:113164200-113180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
8	chr1:113168000-113180000	Weak transcription	Aorta	Aorta
9	chr1:113168800-113180000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:113168800-113180000	Weak transcription	Lung	lung
11	chr1:113168800-113187200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:113168800-113189800	Weak transcription	Fetal Lung	lung
13	chr1:113168800-113191000	Weak transcription	Ovary	ovary
14	chr1:113168800-113199800	Weak transcription	Esophagus	oesophagus
15	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
16	chr1:113169000-113181600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:113169000-113186400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:113169000-113189800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:113169200-113188400	Weak transcription	Left Ventricle	heart
20	chr1:113169800-113188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:113172200-113180000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:113172200-113181000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:113172600-113191400	Weak transcription	Brain Germinal Matrix	brain
24	chr1:113173400-113186600	Weak transcription	Thymus	Thymus
25	chr1:113173400-113186800	Weak transcription	Fetal Stomach	stomach
26	chr1:113174000-113180800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr1:113174400-113179600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:113174400-113181800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:113174400-113186000	Weak transcription	Fetal Thymus	thymus
30	chr1:113174400-113190000	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:113175200-113188800	Weak transcription	Gastric	stomach
32	chr1:113175200-113189800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:113175200-113199800	Weak transcription	Psoas Muscle	Psoas
34	chr1:113175200-113200000	Weak transcription	Right Atrium	heart
35	chr1:113175800-113181200	Enhancers	HepG2	liver
36	chr1:113176000-113199200	Weak transcription	Fetal Brain Female	brain
37	chr1:113176200-113181000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:113176200-113181000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr1:113176200-113185000	Weak transcription	Dnd41	blood
40	chr1:113176800-113180200	Enhancers	Liver	Liver
41	chr1:113177000-113180000	Enhancers	NHEK	skin
42	chr1:113177400-113180600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:113177400-113181000	Enhancers	Hela-S3	cervix
44	chr1:113177400-113181400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:113177800-113179800	Enhancers	Primary hematopoietic stem cells	blood
46	chr1:113177800-113180200	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr1:113177800-113181000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:113177800-113181200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:113177800-113181400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:113178000-113179600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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