Variant report

Variant	rs2759387
Chromosome Location	chr6:163839668-163839669
allele	A/G
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	STAT3	chr6:163839332-163839718	MCF10A-Er-Src	breast:	n/a	n/a
2	TBL1XR1	chr6:163839505-163840983	K562	blood:	n/a	n/a
3	ARID3A	chr6:163839394-163841682	K562	blood:	n/a	chr6:163840686-163840702
4	POLR2A	chr6:163839347-163839767	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:163838578..163840743-chr6:164003751..164005658,2	K562	blood:
2	chr6:163838995..163843341-chr6:163850269..163853237,5	K562	blood:
3	chr6:163836144..163840696-chr6:163983068..163987938,4	K562	blood:
4	chr6:163837764..163839976-chr6:164521625..164524241,2	K562	blood:
5	chr6:163602182..163604039-chr6:163839596..163841553,2	MCF-7	breast:

Variant related genes	Relation type
QKI	TF binding region
CAHM	TF binding region
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1003528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1016501	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1016502	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040514	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047944	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11752044	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194023	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230321	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234603	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234604	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1234976	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614795	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619076	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619863	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629251	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737317	1.00[CHB][hapmap]
rs1737323	1.00[CHB][hapmap]
rs1737329	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737333	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737600	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737601	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737603	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737604	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737606	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737607	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737609	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1737612	1.00[ASN][1000 genomes]
rs1744924	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744925	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744926	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744927	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1744928	1.00[ASN][1000 genomes]
rs1744933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1745094	1.00[ASN][1000 genomes]
rs1764008	1.00[CHB][hapmap]
rs2038146	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038147	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038148	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2057003	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2092406	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092407	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103671	0.83[EUR][1000 genomes]
rs2179523	1.00[ASN][1000 genomes]
rs2179524	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2321698	1.00[ASN][1000 genomes]
rs2321700	1.00[ASN][1000 genomes]
rs2321701	1.00[ASN][1000 genomes]
rs2321702	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484877	1.00[ASN][1000 genomes]
rs2744420	1.00[ASN][1000 genomes]
rs2744421	1.00[ASN][1000 genomes]
rs2745364	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745365	1.00[ASN][1000 genomes]
rs2757579	1.00[ASN][1000 genomes]
rs2757580	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757581	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2757582	1.00[ASN][1000 genomes]
rs2757583	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757586	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757587	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757588	1.00[CHB][hapmap]
rs2757589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759381	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs2759382	0.82[EUR][1000 genomes]
rs2759383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759385	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759388	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759389	0.86[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759390	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759391	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759392	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2759393	0.87[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759395	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759398	1.00[ASN][1000 genomes]
rs2759399	1.00[ASN][1000 genomes]
rs2784865	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784867	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2784873	1.00[ASN][1000 genomes]
rs2784874	1.00[CHB][hapmap]
rs2874602	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708996	1.00[ASN][1000 genomes]
rs4708997	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs56721804	1.00[ASN][1000 genomes]
rs6455900	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455902	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455903	0.86[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455904	1.00[ASN][1000 genomes]
rs6905852	0.82[EUR][1000 genomes]
rs6906008	0.82[EUR][1000 genomes]
rs6909364	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6909921	0.85[YRI][hapmap]
rs6913113	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914387	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915247	0.87[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924130	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6926584	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6927417	1.00[ASN][1000 genomes]
rs6931049	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs721190	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721191	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746116	1.00[ASN][1000 genomes]
rs7749189	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7752945	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7761088	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768051	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769145	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7775850	1.00[ASN][1000 genomes]
rs7776279	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783136	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783140	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs803613	1.00[ASN][1000 genomes]
rs809155	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813640	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs814143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295222	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295223	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9295224	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347754	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347755	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9347756	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347759	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347763	1.00[ASN][1000 genomes]
rs9355427	1.00[CHB][hapmap]
rs9356117	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356119	1.00[CHB][hapmap]
rs9356120	1.00[ASN][1000 genomes]
rs9356121	1.00[ASN][1000 genomes]
rs9365572	0.84[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365573	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9365574	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs9365577	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9456866	0.85[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9456869	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2759387	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs2759387	QKI	cis	uninvolved skin	skin_eQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163832600-163841400	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr6:163833000-163843400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:163833200-163841000	Active TSS	Fetal Muscle Leg	muscle
4	chr6:163833200-163842000	Active TSS	HSMMtube	muscle
5	chr6:163833400-163839800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:163833400-163839800	Active TSS	Fetal Muscle Trunk	muscle
7	chr6:163833400-163840400	Active TSS	Fetal Brain Female	brain
8	chr6:163833400-163840600	Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr6:163833400-163841400	Active TSS	Stomach Smooth Muscle	stomach
10	chr6:163833400-163841400	Active TSS	NHLF	lung
11	chr6:163833400-163843600	Active TSS	Right Ventricle	heart
12	chr6:163833600-163840000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:163833600-163840400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:163833600-163841400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:163833600-163841400	Active TSS	HSMM	muscle
16	chr6:163833600-163842400	Active TSS	Psoas Muscle	Psoas
17	chr6:163833600-163843000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:163833800-163839800	Active TSS	Left Ventricle	heart
19	chr6:163833800-163840000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:163833800-163840800	Active TSS	K562	blood
21	chr6:163833800-163841600	Active TSS	Ovary	ovary
22	chr6:163834000-163840800	Active TSS	GM12878-XiMat	blood
23	chr6:163834200-163841000	Active TSS	HMEC	breast
24	chr6:163834200-163841400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:163835000-163841600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:163836200-163840800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr6:163836200-163840800	Active TSS	Fetal Heart	heart
28	chr6:163836200-163841400	Active TSS	Brain Anterior Caudate	brain
29	chr6:163836200-163841400	Active TSS	Brain Substantia Nigra	brain
30	chr6:163836200-163843400	Active TSS	Brain Angular Gyrus	brain
31	chr6:163836800-163841400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:163837000-163840400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:163837000-163840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:163837000-163841400	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr6:163837000-163843400	Active TSS	Right Atrium	heart
36	chr6:163837400-163857200	Weak transcription	Spleen	Spleen
37	chr6:163837800-163840800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:163837800-163840800	Weak transcription	Stomach Mucosa	stomach
39	chr6:163837800-163842000	Active TSS	Brain Cingulate Gyrus	brain
40	chr6:163837800-163842200	Active TSS	Brain Hippocampus Middle	brain
41	chr6:163837800-163843400	Weak transcription	Gastric	stomach
42	chr6:163837800-163851000	Weak transcription	Small Intestine	intestine
43	chr6:163838000-163839800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:163838000-163840000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr6:163838000-163840200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:163838000-163840400	Active TSS	Fetal Brain Male	brain
47	chr6:163838000-163840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:163838000-163840600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:163838000-163841000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:163838000-163841400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links