Variant report

Variant	rs11968064
Chromosome Location	chr6:107022395-107022396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr6:107022380-107023360	Hela-S3	cervix:	n/a	chr6:107022812-107022821 chr6:107022575-107022584 chr6:107022811-107022820 chr6:107022573-107022587 chr6:107022828-107022836 chr6:107022822-107022842 chr6:107022826-107022837 chr6:107022822-107022842 chr6:107022576-107022585

No.	Distal block	Cell Line	Cell type
1	chr6:106966221..106967730-chr6:107020396..107023333,2	K562	blood:
2	chr6:107015186..107019072-chr6:107020325..107023506,3	K562	blood:
3	chr6:107016200..107018063-chr6:107021199..107023024,2	MCF-7	breast:

Variant related genes	Relation type
RTN4IP1	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1026622	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11759221	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210786	0.99[EUR][1000 genomes]
rs12214557	0.99[EUR][1000 genomes]
rs12523774	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12526141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1419054	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17052215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066202	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs2126395	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2219667	0.90[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2883075	0.94[EUR][1000 genomes]
rs3747790	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4945756	0.82[AMR][1000 genomes]
rs4945758	0.83[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4945759	0.83[MKK][hapmap]
rs4946762	0.80[MKK][hapmap]
rs4946763	0.95[ASN][1000 genomes]
rs4946764	0.89[ASW][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap]
rs4946768	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4946774	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs57424436	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58972320	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911512	0.98[EUR][1000 genomes]
rs7738230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751749	0.99[EUR][1000 genomes]
rs7756852	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9384622	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9384623	0.99[EUR][1000 genomes]
rs9384624	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9386566	0.82[AMR][1000 genomes]
rs9386567	0.98[ASN][1000 genomes]
rs9386571	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs9386574	0.98[EUR][1000 genomes]
rs9398095	0.92[ASN][1000 genomes]
rs9400031	0.99[EUR][1000 genomes]
rs9400032	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9480687	0.98[ASN][1000 genomes]
rs9480692	0.99[EUR][1000 genomes]
rs9486406	0.98[ASN][1000 genomes]
rs9486414	0.81[GIH][hapmap]
rs962476	1.00[CEU][hapmap];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11968064	QRSL1	cis	parietal	SCAN
rs11968064	QRSL1	cis	cerebellum	SCAN
rs11968064	SCML4	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
2	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:106996200-107022400	Weak transcription	Ovary	ovary
4	chr6:106996200-107023000	Weak transcription	Stomach Mucosa	stomach
5	chr6:106996400-107027000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
8	chr6:106996600-107022400	Weak transcription	HUVEC	blood vessel
9	chr6:106999000-107022400	Weak transcription	Right Ventricle	heart
10	chr6:106999200-107022400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:106999800-107030600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:107002400-107023000	Weak transcription	Gastric	stomach
13	chr6:107008400-107027600	Strong transcription	Primary T cells from cord blood	blood
14	chr6:107010200-107064600	Weak transcription	A549	lung
15	chr6:107010600-107022400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:107011800-107030000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:107012600-107022400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:107012800-107030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:107014200-107022400	Weak transcription	Hela-S3	cervix
20	chr6:107014400-107038800	Weak transcription	Fetal Brain Female	brain
21	chr6:107014800-107022400	Weak transcription	Brain Angular Gyrus	brain
22	chr6:107016200-107022400	Weak transcription	Brain Substantia Nigra	brain
23	chr6:107016200-107039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:107016400-107022600	Weak transcription	Brain Anterior Caudate	brain
25	chr6:107017000-107032800	Weak transcription	K562	blood
26	chr6:107017800-107022600	Weak transcription	Lung	lung
27	chr6:107017800-107041000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:107018000-107022400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:107018000-107022400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:107018000-107022400	Weak transcription	HepG2	liver
31	chr6:107018000-107030800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:107018000-107052600	Weak transcription	Colonic Mucosa	Colon
33	chr6:107018200-107022400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:107018400-107022400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:107018400-107066400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:107018400-107076400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:107018600-107022400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:107018600-107022400	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:107018600-107025600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:107018600-107029600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:107018600-107030000	Weak transcription	Fetal Intestine Large	intestine
42	chr6:107018600-107039000	Weak transcription	Placenta	Placenta
43	chr6:107018800-107022600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:107018800-107030200	Weak transcription	Dnd41	blood
45	chr6:107018800-107039400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:107018800-107076200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:107019000-107022600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:107019000-107022800	Weak transcription	Adipose Nuclei	Adipose
49	chr6:107019000-107022800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:107019000-107029200	Weak transcription	Primary hematopoietic stem cells	blood

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