Variant report

Variant	rs2247335
Chromosome Location	chr6:106992592-106992593
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1111830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1613722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1616375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1676008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1676010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1676023	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1676024	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1676026	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1676028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17067603	1.00[JPT][hapmap]
rs17565194	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1770718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770719	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770720	1.00[CEU][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1770721	0.85[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];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770722	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1770723	0.93[ASN][1000 genomes]
rs1770733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2066201	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615209	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747789	0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3804344	1.00[JPT][hapmap]
rs4946762	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6902745	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6911321	1.00[JPT][hapmap]
rs72945076	0.82[ASN][1000 genomes]
rs7771502	0.89[ASN][1000 genomes]
rs783395	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs783396	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs783401	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs783414	1.00[CHB][hapmap]
rs9386565	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[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	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	nsv1017419	chr6:106984669-106997000	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2247335	QRSL1	cis	parietal	SCAN
rs2247335	SCML4	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
3	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:106973600-106992800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:106978800-106993800	Weak transcription	NHLF	lung
6	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
7	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
8	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:106982800-106993200	Weak transcription	HUVEC	blood vessel
10	chr6:106985000-106993800	Weak transcription	NH-A	brain
11	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
12	chr6:106986200-106993400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:106986200-106994000	Weak transcription	Stomach Mucosa	stomach
14	chr6:106986400-106993000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:106986400-106994600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:106986400-106995000	Weak transcription	Thymus	Thymus
17	chr6:106986800-106994400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr6:106987000-106993600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:106987400-106993800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr6:106987600-106993400	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:106987800-106993800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:106988200-106993200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:106988200-106993400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:106988200-106993800	Weak transcription	Esophagus	oesophagus
25	chr6:106988200-107001400	Weak transcription	Lung	lung
26	chr6:106988400-106994000	Strong transcription	GM12878-XiMat	blood
27	chr6:106988400-106995600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:106988600-106992600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:106988600-106993200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:106988800-106994600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr6:106989000-106993200	Strong transcription	HMEC	breast
32	chr6:106989000-106994000	Strong transcription	Fetal Intestine Large	intestine
33	chr6:106989200-106993200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:106989200-106994000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:106989200-106994600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:106989400-106992800	Strong transcription	Primary B cells from cord blood	blood
37	chr6:106989400-106993000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:106989400-106993800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:106989800-106993800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:106989800-106994000	Weak transcription	Hela-S3	cervix
41	chr6:106989800-106995800	Weak transcription	Fetal Stomach	stomach
42	chr6:106990800-106992800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:106991000-106992800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:106991000-106993000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:106991000-106993000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:106991000-106993800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:106991000-106993800	Weak transcription	HSMM	muscle
48	chr6:106991200-106992600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:106991200-106992600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:106991200-106993000	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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