Variant report

Variant	rs6711126
Chromosome Location	chr2:10133728-10133729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:10133680-10133830	HMF	breast:	n/a	n/a
2	CTCF	chr2:10133720-10133870	AG09309	skin:	n/a	n/a
3	CTCF	chr2:10133620-10133770	NHLF	lung:	n/a	n/a
4	CTCF	chr2:10133700-10133850	NHDF-neo	bronchial:	n/a	n/a
5	CTCF	chr2:10133676-10133886	IMR90	lung:	n/a	n/a
6	CTCF	chr2:10133660-10133810	HCM	heart:	n/a	n/a
7	CTCF	chr2:10133700-10133850	AG09309	skin:	n/a	n/a
8	CTCF	chr2:10133700-10133850	AoAF	blood vessel:	n/a	n/a
9	GATA1	chr2:10133565-10134268	PBDE	blood:	n/a	n/a
10	CTCF	chr2:10133720-10133870	AG10803	skin:	n/a	n/a
11	CTCF	chr2:10133700-10133850	HMF	breast:	n/a	n/a
12	CTCF	chr2:10133720-10133870	AG09319	gingival:	n/a	n/a
13	FOS	chr2:10133705-10134340	HUVEC	blood vessel:	n/a	chr2:10134085-10134096 chr2:10134165-10134172
14	CTCF	chr2:10133700-10133850	AG04449	skin:	n/a	n/a
15	CTCF	chr2:10133700-10133850	AG10803	skin:	n/a	n/a
16	CTCF	chr2:10133640-10133790	HFF	foreskin:	n/a	n/a
17	GATA2	chr2:10133626-10134452	HUVEC	blood vessel:	n/a	n/a
18	CTCF	chr2:10133720-10133870	AG04449	skin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10119873..10122415-chr2:10133377..10135043,2	K562	blood:
2	chr2:10124756..10127578-chr2:10133279..10134788,2	K562	blood:

No data

Variant related genes	Relation type
GRHL1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11674576	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690988	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883961	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886114	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886486	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887890	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889061	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902236	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11902932	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401891	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867262	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16867266	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17455130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897164	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012320	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116014	0.94[ASN][1000 genomes]
rs2116015	0.94[ASN][1000 genomes]
rs2163336	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[ASN][1000 genomes]
rs3791761	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3791763	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791764	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828262	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41264205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482455	0.82[ASN][1000 genomes]
rs4635506	0.82[ASN][1000 genomes]
rs59345896	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66920316	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67093290	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721359	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67223835	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725087	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735737	0.82[ASN][1000 genomes]
rs6739827	0.94[ASN][1000 genomes]
rs6749296	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784430	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72784434	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784441	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784463	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730922	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162262	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162264	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73913937	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73913938	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891499	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6711126	GRHL1	cis	cerebellum	SCAN
rs6711126	GRHL1	cis	multi-tissue	Pritchard

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:10101600-10136400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:10102200-10136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:10113400-10136800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:10113400-10141200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:10124000-10136400	Weak transcription	Hela-S3	cervix
8	chr2:10124400-10139200	Weak transcription	Gastric	stomach
9	chr2:10124800-10143200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
11	chr2:10125000-10134200	Weak transcription	Right Ventricle	heart
12	chr2:10125000-10140600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:10125000-10147600	Weak transcription	K562	blood
14	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
15	chr2:10125200-10134000	Weak transcription	Stomach Mucosa	stomach
16	chr2:10125200-10139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:10125200-10139200	Weak transcription	Pancreas	Pancrea
18	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:10126000-10144000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:10126200-10139200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:10126400-10141200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:10128000-10142800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:10128000-10146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:10128600-10140800	Weak transcription	Fetal Brain Male	brain
25	chr2:10130000-10142000	Strong transcription	HepG2	liver
26	chr2:10130600-10134200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:10130800-10133800	Enhancers	NHDF-Ad	bronchial
28	chr2:10130800-10134000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:10130800-10134000	Enhancers	HSMM	muscle
30	chr2:10130800-10135400	Enhancers	Spleen	Spleen
31	chr2:10130800-10138600	Enhancers	Fetal Muscle Leg	muscle
32	chr2:10131200-10133800	Weak transcription	Lung	lung
33	chr2:10131400-10134400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr2:10131400-10134400	Genic enhancers	Placenta	Placenta
35	chr2:10131400-10134800	Enhancers	Fetal Stomach	stomach
36	chr2:10131600-10141200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:10131600-10149600	Weak transcription	Brain Substantia Nigra	brain
38	chr2:10131800-10133800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:10131800-10134000	Enhancers	Fetal Kidney	kidney
40	chr2:10131800-10137200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:10132200-10134800	Enhancers	Fetal Muscle Trunk	muscle
42	chr2:10132200-10145200	Weak transcription	Fetal Intestine Large	intestine
43	chr2:10132200-10146800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:10132400-10134000	Strong transcription	Liver	Liver
45	chr2:10132400-10134200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:10132400-10134600	Weak transcription	Fetal Intestine Small	intestine
47	chr2:10132400-10146400	Weak transcription	Left Ventricle	heart
48	chr2:10132400-10146800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:10132600-10135800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:10132600-10136600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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