Variant report

Variant	rs6953290
Chromosome Location	chr7:7786122-7786123
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	TCF7L2	chr7:7786109-7786562	PANC-1	pancreas:	n/a	n/a
2	GATA3	chr7:7786041-7786339	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
RPL23AP51	TF binding region
ENSG00000234718	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10486186	0.85[ASN][1000 genomes]
rs10952069	0.84[ASN][1000 genomes]
rs11766846	0.85[ASN][1000 genomes]
rs12154236	0.83[ASN][1000 genomes]
rs12154244	0.85[ASN][1000 genomes]
rs12154665	0.84[ASN][1000 genomes]
rs12154979	0.84[ASN][1000 genomes]
rs12702640	0.83[ASN][1000 genomes]
rs12702642	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12702643	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13222137	0.84[ASN][1000 genomes]
rs13234233	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13237260	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13237271	0.84[ASN][1000 genomes]
rs13244344	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17136953	0.84[ASN][1000 genomes]
rs17136957	0.84[ASN][1000 genomes]
rs17137036	0.85[ASN][1000 genomes]
rs17137255	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17137257	0.80[EUR][1000 genomes]
rs2024372	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2024373	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2068637	0.81[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2110556	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2241075	0.81[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs34627388	0.84[ASN][1000 genomes]
rs34881338	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35562533	0.86[ASN][1000 genomes]
rs35718996	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35844437	0.84[ASN][1000 genomes]
rs35897634	0.80[EUR][1000 genomes]
rs36045810	0.84[ASN][1000 genomes]
rs36092641	0.83[ASN][1000 genomes]
rs4725019	0.85[ASN][1000 genomes]
rs4725022	0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4725023	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62432645	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6958302	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6971799	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6972438	0.84[ASN][1000 genomes]
rs717298	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs73676911	0.81[ASN][1000 genomes]
rs73676912	0.81[ASN][1000 genomes]
rs7796096	0.84[ASN][1000 genomes]
rs972647	0.81[ASN][1000 genomes]
rs974989	0.89[ASN][1000 genomes]
rs974990	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv887483	chr7:7682439-7798217	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv1026564	chr7:7734846-7897847	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv887487	chr7:7740914-7802561	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv887488	chr7:7770203-7794484	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv887489	chr7:7770203-7913311	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7752600-7790400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:7759400-7791200	Weak transcription	Esophagus	oesophagus
3	chr7:7759600-7786800	Weak transcription	Aorta	Aorta
4	chr7:7771600-7791000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:7773000-7802000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:7778600-7797400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:7779000-7787200	Weak transcription	Small Intestine	intestine
8	chr7:7779600-7786400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:7779800-7796000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:7779800-7800200	Weak transcription	Thymus	Thymus
11	chr7:7783000-7791200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:7784800-7786200	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:7784800-7786200	Enhancers	Stomach Mucosa	stomach
14	chr7:7784800-7786600	Enhancers	Stomach Smooth Muscle	stomach
15	chr7:7784800-7787200	Enhancers	Fetal Heart	heart
16	chr7:7785000-7786600	Enhancers	Colon Smooth Muscle	Colon
17	chr7:7785400-7786200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr7:7785400-7787200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr7:7785600-7786400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:7785600-7786400	Enhancers	Fetal Thymus	thymus
21	chr7:7785600-7800800	Weak transcription	Primary B cells from cord blood	blood
22	chr7:7785800-7786200	Enhancers	Fetal Intestine Small	intestine
23	chr7:7785800-7786600	Enhancers	Duodenum Mucosa	Duodenum
24	chr7:7785800-7791200	Weak transcription	Psoas Muscle	Psoas
25	chr7:7786000-7786400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr7:7786000-7786400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:7786000-7786400	Enhancers	Brain Germinal Matrix	brain
28	chr7:7786000-7786400	Enhancers	Fetal Brain Female	brain
29	chr7:7786000-7786600	Enhancers	Rectal Smooth Muscle	rectum
30	chr7:7786000-7791200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links