Variant report

Variant	rs3756879
Chromosome Location	chr6:163990308-163990309
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163832753..163835085-chr6:163989937..163992434,2	MCF-7	breast:
2	chr6:163974907..163977416-chr6:163988942..163991907,2	K562	blood:
3	chr6:163989917..163992171-chr6:164159430..164162397,2	K562	blood:
4	chr6:163833058..163837205-chr6:163990300..163993752,7	K562	blood:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1047935	0.82[ASN][1000 genomes]
rs11962088	0.88[CHB][hapmap]
rs13199835	0.82[ASN][1000 genomes]
rs16895015	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs1737328	0.83[CHB][hapmap]
rs17591955	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs2143358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294698	0.82[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2294703	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294706	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2294707	0.82[EUR][1000 genomes]
rs2294709	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3763197	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs41268571	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4709716	0.84[CHB][hapmap]
rs4709717	0.82[CHB][hapmap]
rs4709722	0.83[ASN][1000 genomes]
rs59759961	0.82[ASN][1000 genomes]
rs6931903	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs6939218	0.88[CHB][hapmap]
rs715020	0.88[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs7758706	0.87[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap]
rs7772756	0.93[CHB][hapmap]
rs9346960	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs9347760	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9364689	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs9364691	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs9364692	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3756879	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
2	chr6:163949600-163992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:163949600-163995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:163951200-163993200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:163952600-163996600	Weak transcription	Gastric	stomach
6	chr6:163954000-163991600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:163958200-163991600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:163959800-163997200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:163960600-163993000	Weak transcription	A549	lung
10	chr6:163965600-163995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:163968800-163991800	Weak transcription	Fetal Brain Male	brain
12	chr6:163969000-163991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:163970400-163991600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:163970800-164000200	Weak transcription	Right Atrium	heart
15	chr6:163972600-163995600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:163974000-163997000	Weak transcription	Fetal Intestine Small	intestine
17	chr6:163974200-163997000	Weak transcription	Fetal Intestine Large	intestine
18	chr6:163976000-163993200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:163977000-163993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:163978000-163998000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr6:163978800-163997600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr6:163979200-163996200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:163979800-163990600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:163980000-163991600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:163980000-163991600	Weak transcription	Thymus	Thymus
26	chr6:163980000-163997200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:163980200-163991600	Weak transcription	Lung	lung
28	chr6:163980200-163996000	Weak transcription	Small Intestine	intestine
29	chr6:163980400-163991600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:163982600-163994000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:163982800-163996800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:163982800-163998000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:163983000-163998400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:163983200-163993400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:163983200-163997400	Weak transcription	Fetal Brain Female	brain
36	chr6:163983600-163991800	Weak transcription	Fetal Kidney	kidney
37	chr6:163984200-163991200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:163984200-163993400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr6:163984800-163991600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:163984800-163991800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:163984800-163994000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:163984800-163995000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:163984800-163995400	Weak transcription	Psoas Muscle	Psoas
44	chr6:163984800-164000000	Weak transcription	Right Ventricle	heart
45	chr6:163985000-163991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:163985000-163991600	Weak transcription	Ovary	ovary
47	chr6:163985000-163991600	Weak transcription	Pancreas	Pancrea
48	chr6:163985000-164006800	Weak transcription	Spleen	Spleen
49	chr6:163985400-163991600	Weak transcription	NHLF	lung
50	chr6:163985400-163991800	Weak transcription	NHEK	skin

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