Variant report

Variant	rs6939187
Chromosome Location	chr6:163829535-163829536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163825837..163828170-chr6:163829514..163831485,3	MCF-7	breast:
2	chr6:163828630..163831846-chr6:163832456..163835653,4	MCF-7	breast:
3	chr6:163824877..163830472-chr6:163836413..163839637,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12210561	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1230320	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1234977	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13211340	0.93[ASN][1000 genomes]
rs1541141	0.93[ASN][1000 genomes]
rs1572434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614869	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1737330	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737610	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1744929	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1764022	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764023	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2259476	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2259477	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475390	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2475877	0.87[EUR][1000 genomes]
rs2757575	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757576	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757584	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2757585	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2759386	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2759396	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4709715	0.93[ASN][1000 genomes]
rs73021476	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs768662	0.93[ASN][1000 genomes]
rs7767891	0.93[ASN][1000 genomes]
rs783137	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs783139	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs803612	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9347747	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9347752	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9347765	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9347766	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9365565	0.93[ASN][1000 genomes]
rs9365575	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9458820	0.93[ASN][1000 genomes]
rs9458843	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv1791729	chr6:163814557-163836689	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1839403	chr6:163822296-163835490	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1793461	chr6:163822296-163836634	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1794611	chr6:163822296-163836689	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv1796475	chr6:163822296-163836689	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv1797016	chr6:163822296-163836689	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1801202	chr6:163822296-163836689	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1801861	chr6:163822296-163836689	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv605193	chr6:163824864-163835490	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv605194	chr6:163824864-163836293	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv605195	chr6:163824864-163836634	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6939187	QKI	cis	Whole Blood	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163827000-163832000	Weak transcription	Gastric	stomach
2	chr6:163827200-163830800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:163827200-163832000	Weak transcription	Placenta	Placenta
4	chr6:163827200-163832000	Weak transcription	Lung	lung
5	chr6:163827200-163833600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:163827200-163833600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:163827200-163833800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:163827200-163834200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:163827200-163834200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:163827200-163834200	Weak transcription	Spleen	Spleen
11	chr6:163827400-163829600	Weak transcription	A549	lung
12	chr6:163827400-163830400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:163827400-163830800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:163827400-163832400	Weak transcription	Left Ventricle	heart
15	chr6:163827400-163833000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:163827400-163833400	Weak transcription	HSMM	muscle
17	chr6:163827400-163833600	Weak transcription	Psoas Muscle	Psoas
18	chr6:163827400-163833600	Weak transcription	Right Atrium	heart
19	chr6:163827400-163833800	Weak transcription	Aorta	Aorta
20	chr6:163827600-163829600	Enhancers	HepG2	liver
21	chr6:163827600-163832000	Weak transcription	HSMMtube	muscle
22	chr6:163827600-163833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:163827600-163833400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:163827600-163833400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:163827600-163833400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:163827600-163833400	Weak transcription	Fetal Lung	lung
27	chr6:163827600-163833400	Weak transcription	Fetal Stomach	stomach
28	chr6:163827600-163833400	Weak transcription	NHLF	lung
29	chr6:163827600-163833800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:163827800-163830000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:163827800-163830400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:163827800-163833400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:163827800-163833400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:163827800-163833400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:163827800-163833400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:163827800-163833400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:163828000-163833200	Weak transcription	HUVEC	blood vessel
38	chr6:163828000-163833600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:163828200-163829600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:163828200-163832600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:163828200-163832600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:163828200-163833000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:163828200-163833400	Weak transcription	Liver	Liver
44	chr6:163828200-163833400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:163828200-163833400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:163828200-163833400	Weak transcription	Right Ventricle	heart
47	chr6:163828200-163833400	Weak transcription	GM12878-XiMat	blood
48	chr6:163828200-163833600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:163828400-163832000	Weak transcription	Brain Substantia Nigra	brain
50	chr6:163828600-163833000	Weak transcription	Adipose Nuclei	Adipose

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