Variant report

Variant	rs7762601
Chromosome Location	chr6:36871732-36871733
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36867430..36871951-chr6:36875008..36877997,4	K562	blood:
2	chr6:36871006..36873837-chr6:36953580..36955974,2	K562	blood:
3	chr6:36860505..36863428-chr6:36870664..36872408,2	MCF-7	breast:
4	chr6:36852943..36861433-chr6:36865588..36872573,10	K562	blood:
5	chr6:36560719..36562370-chr6:36870379..36872149,2	K562	blood:
6	chr6:36852581..36854443-chr6:36870152..36872140,2	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10456445	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456447	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10456448	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947646	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947648	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11964396	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12111266	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12111291	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12191780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193721	0.82[ASN][1000 genomes]
rs12195012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211502	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12215873	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524018	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524422	0.84[CEU][hapmap]
rs12524649	1.00[ASN][1000 genomes]
rs12525180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525540	0.84[CEU][hapmap]
rs12529199	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs12529769	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17374068	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs17552561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272192	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41408445	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs4348312	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4714013	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs4714022	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55928881	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56240344	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56302344	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66474948	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72846078	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7745555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7762601	C6orf89	cis	lymphoblastoid	seeQTL
rs7762601	C6orf89	cis	parietal	SCAN
rs7762601	PNPLA1	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36873600	Weak transcription	Aorta	Aorta
2	chr6:36854200-36881000	Weak transcription	Gastric	stomach
3	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:36854800-36875200	Weak transcription	Esophagus	oesophagus
6	chr6:36854800-36881000	Weak transcription	A549	lung
7	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:36855400-36881000	Weak transcription	Small Intestine	intestine
10	chr6:36857000-36874400	Weak transcription	Pancreas	Pancrea
11	chr6:36859600-36879400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:36861200-36879000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr6:36862000-36875800	Strong transcription	Dnd41	blood
14	chr6:36864600-36871800	Strong transcription	Fetal Stomach	stomach
15	chr6:36864600-36881200	Strong transcription	Fetal Intestine Small	intestine
16	chr6:36865400-36873200	Strong transcription	Primary T cells from cord blood	blood
17	chr6:36865400-36874200	Strong transcription	Fetal Muscle Leg	muscle
18	chr6:36865400-36876600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:36866000-36875800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:36866000-36876800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:36866000-36877200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:36866200-36874200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr6:36866200-36876800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:36866200-36877600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr6:36866200-36878400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:36866400-36877800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:36866600-36876000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:36866600-36876200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:36866600-36878400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:36866600-36878400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:36866800-36872600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:36866800-36874400	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:36866800-36876000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:36866800-36881600	Strong transcription	Fetal Intestine Large	intestine
36	chr6:36867000-36874400	Strong transcription	Thymus	Thymus
37	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:36867200-36872200	Strong transcription	NHDF-Ad	bronchial
39	chr6:36867200-36873000	Weak transcription	Fetal Heart	heart
40	chr6:36867800-36872600	Weak transcription	Spleen	Spleen
41	chr6:36868600-36871800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:36868600-36872200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:36868600-36882000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:36869000-36871800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:36869000-36871800	Weak transcription	Lung	lung
46	chr6:36869000-36871800	Weak transcription	Ovary	ovary
47	chr6:36869000-36872600	Weak transcription	Right Ventricle	heart
48	chr6:36869600-36872200	Strong transcription	Brain Substantia Nigra	brain
49	chr6:36869600-36872200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:36869600-36872400	Strong transcription	Brain Hippocampus Middle	brain

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