Variant report

Variant	rs13218960
Chromosome Location	chr6:106983465-106983466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106982665..106985601-chr6:106993025..106995759,2	MCF-7	breast:
2	chr6:106982668..106985044-chr6:106987673..106989483,2	K562	blood:
3	chr6:106972979..106975776-chr6:106983451..106985409,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1057433	0.86[AMR][1000 genomes]
rs1159148	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13193036	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13194986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13202166	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13202942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207381	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13218830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13219061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs17495644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17495720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17560979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1841688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1841689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870866	0.82[ASN][1000 genomes]
rs2054365	1.00[CHB][hapmap]
rs2297970	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2306099	0.89[ASN][1000 genomes]
rs2353050	0.85[ASN][1000 genomes]
rs34590393	0.89[ASN][1000 genomes]
rs35090908	0.85[ASN][1000 genomes]
rs35452551	0.85[ASN][1000 genomes]
rs35546863	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35790766	0.82[ASN][1000 genomes]
rs35843244	0.89[ASN][1000 genomes]
rs55858175	0.82[ASN][1000 genomes]
rs56361614	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72941340	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7752730	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7756087	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs783394	0.87[ASW][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap]
rs783397	0.87[ASW][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap]
rs9320173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320175	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486385	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486386	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486388	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv3407164	chr6:106982684-106985232	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv2481074	chr6:106982686-106984346	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	esv3418513	chr6:106982959-106984957	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	esv6147	chr6:106983388-106984219	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv2278880	chr6:106983439-106984156	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	esv3356248	chr6:106983459-106984457	Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13218960	QRSL1	cis	multi-tissue	Pritchard
rs13218960	QRSL1	cis	Thyroid	GTEx
rs13218960	QRSL1	cis	lymphoblastoid	seeQTL
rs13218960	QRSL1	cis	Esophagus Muscularis	GTEx
rs13218960	RTN4IP1	cis	parietal	SCAN
rs13218960	QRSL1	cis	Nerve Tibial	GTEx
rs13218960	QRSL1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-106991000	Weak transcription	Spleen	Spleen
3	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
4	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:106973400-106985600	Weak transcription	Stomach Mucosa	stomach
6	chr6:106973600-106985800	Weak transcription	Thymus	Thymus
7	chr6:106973600-106986000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:106973600-106992800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:106976400-106986200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:106976600-106991400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:106977000-106986400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:106978800-106984200	Weak transcription	NH-A	brain
13	chr6:106978800-106985600	Weak transcription	Fetal Thymus	thymus
14	chr6:106978800-106993800	Weak transcription	NHLF	lung
15	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
16	chr6:106979600-106984200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:106979600-106987200	Weak transcription	HepG2	liver
18	chr6:106980200-106984400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:106980800-106984400	Genic enhancers	HMEC	breast
20	chr6:106980800-106986200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:106980800-106986400	Strong transcription	Liver	Liver
22	chr6:106981200-106984600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:106981400-106988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:106981600-106984600	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
26	chr6:106981800-106983600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:106981800-106984000	Weak transcription	Fetal Intestine Small	intestine
28	chr6:106981800-106985200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:106981800-106985600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:106981800-106985600	Weak transcription	Esophagus	oesophagus
31	chr6:106981800-106987800	Weak transcription	Lung	lung
32	chr6:106982200-106984200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:106982400-106984600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:106982400-106984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:106982400-106984800	Genic enhancers	NHEK	skin
36	chr6:106982400-106986000	Weak transcription	Placenta	Placenta
37	chr6:106982400-106987400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:106982400-106987600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:106982400-106987800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:106982600-106984000	Weak transcription	Primary T cells from cord blood	blood
42	chr6:106982600-106984000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr6:106982600-106984000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:106982600-106984000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:106982600-106984000	Weak transcription	NHDF-Ad	bronchial
46	chr6:106982600-106984200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:106982600-106984400	Strong transcription	Primary B cells from cord blood	blood
48	chr6:106982600-106984600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:106982600-106985600	Weak transcription	Fetal Intestine Large	intestine
50	chr6:106982600-106987200	Weak transcription	Hela-S3	cervix

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