Variant report

Variant	rs7750294
Chromosome Location	chr6:53924170-53924171
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11965692	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs13196588	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13199742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13211062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13211796	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1359562	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs1409110	0.90[CEU][hapmap]
rs35395359	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778106	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36057920	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57712770	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71558851	0.83[EUR][1000 genomes]
rs71558852	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71558853	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7739196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296735	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9464021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9474710	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9474715	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.92[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv603110	chr6:53885918-54103794	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1027036	chr6:53912335-53931843	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
10	nsv7901	chr6:53914491-53981080	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv823691	chr6:53918427-53978766	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1825401	chr6:53920024-53934260	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
13	nsv885885	chr6:53920024-54046264	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1030908	chr6:53920595-53931843	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7750294	ICK	cis	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53913600-53926000	Weak transcription	Left Ventricle	heart
2	chr6:53918800-53925200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:53919400-53928200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:53919600-53924400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:53919600-53924400	Weak transcription	HUVEC	blood vessel
6	chr6:53919600-53924400	Weak transcription	Osteobl	bone
7	chr6:53919600-53924600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:53919600-53924600	Weak transcription	Hela-S3	cervix
9	chr6:53919600-53924600	Weak transcription	NHLF	lung
10	chr6:53919600-53928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:53919600-53928400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:53919600-53928400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:53919800-53925000	Weak transcription	HSMM	muscle
14	chr6:53921200-53924600	Enhancers	Liver	Liver
15	chr6:53921400-53926000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:53921600-53936600	Weak transcription	Right Ventricle	heart
17	chr6:53922200-53928000	Weak transcription	Adipose Nuclei	Adipose
18	chr6:53922400-53924200	Enhancers	Fetal Intestine Large	intestine
19	chr6:53923200-53924200	Enhancers	Fetal Intestine Small	intestine
20	chr6:53923200-53924200	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr6:53923200-53924200	Enhancers	Small Intestine	intestine
22	chr6:53923400-53924600	Weak transcription	Right Atrium	heart
23	chr6:53923600-53924200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:53923600-53924400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:53923800-53924200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:53923800-53924200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr6:53923800-53924400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:53923800-53927600	Enhancers	Fetal Heart	heart
29	chr6:53924000-53924200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr6:53924000-53924800	Enhancers	Colon Smooth Muscle	Colon
31	chr6:53924000-53925400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:53924000-53935200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links