Variant report

Variant	rs3747790
Chromosome Location	chr6:107016731-107016732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:107016200..107018063-chr6:107021199..107023024,2	MCF-7	breast:
2	chr6:106891408..106894325-chr6:107016587..107019305,2	MCF-7	breast:
3	chr6:107014621..107016841-chr6:107018456..107020418,2	MCF-7	breast:
4	chr6:107015186..107019072-chr6:107020325..107023506,3	K562	blood:
5	chr6:107015342..107016968-chr6:107029382..107032142,2	K562	blood:

Variant related genes	Relation type
ENSG00000130347	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1037955	0.90[CEU][hapmap];0.87[GIH][hapmap]
rs1057429	0.80[EUR][1000 genomes]
rs1135384	0.80[EUR][1000 genomes]
rs11751653	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11758586	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11759221	0.98[ASN][1000 genomes]
rs11968064	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12523774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12526141	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs13319	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs1419054	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes]
rs1676016	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs17052211	0.80[EUR][1000 genomes]
rs17052215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17067345	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17067368	0.92[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17067424	0.90[AFR][1000 genomes]
rs17067430	0.88[AFR][1000 genomes]
rs1770728	0.81[CEU][hapmap]
rs1770731	0.86[YRI][hapmap]
rs1770732	0.81[CEU][hapmap]
rs2054366	0.90[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs2066202	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126395	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2219667	0.88[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2297971	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs2615206	0.90[CEU][hapmap]
rs2615207	0.90[CEU][hapmap];0.87[GIH][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap]
rs2642469	0.88[CEU][hapmap]
rs4440506	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4516976	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4523123	0.92[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4945759	0.90[CEU][hapmap];0.94[TSI][hapmap]
rs4946763	0.94[ASN][1000 genomes]
rs4946764	0.90[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs55702661	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs56120103	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs56257618	0.95[AFR][1000 genomes]
rs57110857	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs57332679	0.80[EUR][1000 genomes]
rs57424436	0.98[ASN][1000 genomes]
rs58742517	0.80[EUR][1000 genomes]
rs58972320	0.98[ASN][1000 genomes]
rs59698263	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs60052218	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs60505757	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs60533767	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs61465560	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs66579211	0.90[AFR][1000 genomes]
rs66607211	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs67671335	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6903754	0.90[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6907164	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6909966	0.80[EUR][1000 genomes]
rs6910512	0.80[EUR][1000 genomes]
rs6913374	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6914306	0.90[AFR][1000 genomes]
rs6919137	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6922741	0.80[EUR][1000 genomes]
rs6926307	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6926670	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6926833	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6926888	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6933677	0.80[EUR][1000 genomes]
rs6940963	0.80[EUR][1000 genomes]
rs7451968	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7738230	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7741101	0.90[CEU][hapmap];0.97[TSI][hapmap]
rs7770930	0.90[CEU][hapmap]
rs7776287	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7776294	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs8013	0.90[CEU][hapmap];0.87[GIH][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs9320182	0.90[CEU][hapmap];0.87[GIH][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs9320183	0.92[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9384622	0.96[ASN][1000 genomes]
rs9386567	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398095	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9480684	0.84[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9480685	0.90[CEU][hapmap]
rs9480686	0.92[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9480687	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480688	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9480689	0.92[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486396	0.94[AFR][1000 genomes]
rs9486397	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486398	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9486399	0.90[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486400	0.87[GIH][hapmap];0.85[MKK][hapmap]
rs9486401	0.80[EUR][1000 genomes]
rs9486403	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs9486404	0.90[CEU][hapmap];0.87[GIH][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs9486406	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486407	0.80[EUR][1000 genomes]
rs9486408	0.80[EUR][1000 genomes]
rs9486409	0.80[EUR][1000 genomes]
rs9486410	0.90[CEU][hapmap];0.87[GIH][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs9486411	0.90[CEU][hapmap];0.87[GIH][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs9486412	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486413	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486414	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486415	0.84[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486416	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486417	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9486418	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs965347	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9689006	0.90[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3747790	QRSL1	cis	cerebellum	SCAN

Chromatin state (count:108 , 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	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
4	chr6:106994000-107017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:106994200-107019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:106994200-107019600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr6:106995000-107019400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:106995200-107018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:106996200-107017200	Weak transcription	HSMM	muscle
10	chr6:106996200-107018400	Weak transcription	Fetal Stomach	stomach
11	chr6:106996200-107022400	Weak transcription	Ovary	ovary
12	chr6:106996200-107023000	Weak transcription	Stomach Mucosa	stomach
13	chr6:106996400-107027000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
16	chr6:106996600-107018400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:106996600-107022400	Weak transcription	HUVEC	blood vessel
18	chr6:106999000-107022400	Weak transcription	Right Ventricle	heart
19	chr6:106999200-107022400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:106999800-107030600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:107000400-107018800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:107000800-107021200	Strong transcription	Primary B cells from cord blood	blood
23	chr6:107001400-107018600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:107002200-107019000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:107002200-107020200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:107002200-107020200	Weak transcription	Pancreas	Pancrea
27	chr6:107002400-107023000	Weak transcription	Gastric	stomach
28	chr6:107002800-107017400	Weak transcription	Lung	lung
29	chr6:107003800-107019400	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:107005000-107018800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr6:107005000-107021400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:107005000-107021800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:107005200-107019200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:107006200-107019800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:107006800-107019000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:107008400-107027600	Strong transcription	Primary T cells from cord blood	blood
37	chr6:107008600-107018800	Strong transcription	Dnd41	blood
38	chr6:107009400-107017400	Weak transcription	Left Ventricle	heart
39	chr6:107010200-107017200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:107010200-107064600	Weak transcription	A549	lung
41	chr6:107010600-107022400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:107010800-107019000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:107011400-107018000	Strong transcription	HepG2	liver
44	chr6:107011400-107019400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:107011800-107018000	Weak transcription	Fetal Lung	lung
46	chr6:107011800-107030000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:107012000-107020600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:107012400-107017400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:107012600-107017200	Weak transcription	Spleen	Spleen
50	chr6:107012600-107017400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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