Variant report

Variant	rs3734351
Chromosome Location	chr6:101307131-101307132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101299454..101302050-chr6:101304670..101307311,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12527901	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12664068	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1854483	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4098482	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56115902	0.93[ASN][1000 genomes]
rs57454377	0.87[ASN][1000 genomes]
rs57795969	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61289570	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916271	0.91[AFR][1000 genomes]
rs6927027	0.94[GIH][hapmap]
rs6930051	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72610823	0.98[ASN][1000 genomes]
rs72610824	0.82[ASN][1000 genomes]
rs7748160	0.83[ASN][1000 genomes]
rs9377233	0.90[CHB][hapmap]
rs9377246	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9377247	0.85[ASN][1000 genomes]
rs9386259	0.84[ASW][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs9386260	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9386262	0.81[ASN][1000 genomes]
rs9390697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390699	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9390700	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9399696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404063	0.85[ASN][1000 genomes]
rs9485415	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9498392	0.90[CHB][hapmap]
rs9498408	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9498409	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498411	0.86[AFR][1000 genomes]
rs9498414	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9498418	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9498439	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9791284	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3734351	GRIK2	cis	Artery Tibial	GTEx
rs3734351	ASCC3	cis	Nerve Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101215200-101311400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:101275800-101314400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:101278000-101313800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:101281200-101317000	Weak transcription	Small Intestine	intestine
6	chr6:101282000-101311400	Weak transcription	Aorta	Aorta
7	chr6:101285600-101326600	Weak transcription	NHLF	lung
8	chr6:101287800-101313000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:101290200-101318200	Weak transcription	Fetal Lung	lung
10	chr6:101290600-101312800	Weak transcription	Fetal Brain Male	brain
11	chr6:101290800-101311400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:101290800-101311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
14	chr6:101291400-101314000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:101291600-101314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:101291800-101312800	Weak transcription	Gastric	stomach
17	chr6:101292600-101310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:101294000-101320400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:101294200-101314200	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:101294600-101310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:101294600-101311400	Weak transcription	Pancreas	Pancrea
22	chr6:101294600-101314400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:101294600-101320600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:101294600-101325400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:101294600-101328600	Weak transcription	Spleen	Spleen
26	chr6:101294800-101325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:101295000-101325800	Weak transcription	Brain Angular Gyrus	brain
28	chr6:101295000-101325800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:101296000-101323400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:101296600-101310000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:101296800-101307200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:101296800-101308400	Weak transcription	Adipose Nuclei	Adipose
33	chr6:101296800-101310200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:101296800-101317000	Weak transcription	HSMMtube	muscle
35	chr6:101296800-101323800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:101297000-101310800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:101297000-101310800	Weak transcription	Fetal Thymus	thymus
38	chr6:101297000-101311400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr6:101297000-101311400	Weak transcription	Left Ventricle	heart
40	chr6:101297000-101327200	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:101297000-101328200	Weak transcription	Ovary	ovary
42	chr6:101300200-101311400	Weak transcription	Thymus	Thymus
43	chr6:101300200-101319000	Weak transcription	Fetal Stomach	stomach
44	chr6:101300200-101326600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:101300200-101328400	Weak transcription	Esophagus	oesophagus
46	chr6:101300200-101328400	Weak transcription	Lung	lung
47	chr6:101300400-101311400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:101302600-101327800	Weak transcription	Stomach Mucosa	stomach
49	chr6:101303000-101314800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:101303200-101316000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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