Variant report

Variant	rs3904720
Chromosome Location	chr6:163831687-163831688
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	POLR2A	chr6:163830868-163832168	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:163831497-163832827	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163828630..163831846-chr6:163832456..163835653,4	MCF-7	breast:
2	chr6:163680711..163682973-chr6:163830679..163833543,2	K562	blood:

Variant related genes	Relation type
QKI	TF binding region
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11962088	0.86[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11964436	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1414724	0.84[AMR][1000 genomes]
rs1591536	0.84[AMR][1000 genomes]
rs16894934	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16895015	0.81[CHB][hapmap]
rs1737319	0.84[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs1737320	0.82[AMR][1000 genomes]
rs1737321	0.84[JPT][hapmap]
rs1737322	0.84[JPT][hapmap]
rs1737324	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs1737328	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	0.81[CHB][hapmap]
rs1764009	0.84[JPT][hapmap]
rs1764010	0.82[MEX][hapmap]
rs1764011	0.83[AMR][1000 genomes]
rs1764015	0.84[AMR][1000 genomes]
rs1764019	0.84[AMR][1000 genomes]
rs2064230	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2064231	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2065857	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2143358	0.81[CHD][hapmap]
rs2294703	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs34979127	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3763197	0.93[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3857504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4263561	0.90[JPT][hapmap]
rs55779730	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56062115	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6931903	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs6939218	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs718878	0.84[AMR][1000 genomes]
rs718879	0.84[AMR][1000 genomes]
rs73013582	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73013591	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73015309	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73015318	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7758706	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs7772756	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9347760	0.83[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3904720	UNC93A	cis	parietal	SCAN
rs3904720	SYNPR	trans	parietal	SCAN
rs3904720	QKI	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:163827200-163832000	Weak transcription	Placenta	Placenta
3	chr6:163827200-163832000	Weak transcription	Lung	lung
4	chr6:163827200-163833600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:163827200-163833600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:163827200-163833800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:163827200-163834200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:163827200-163834200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:163827200-163834200	Weak transcription	Spleen	Spleen
10	chr6:163827400-163832400	Weak transcription	Left Ventricle	heart
11	chr6:163827400-163833000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:163827400-163833400	Weak transcription	HSMM	muscle
13	chr6:163827400-163833600	Weak transcription	Psoas Muscle	Psoas
14	chr6:163827400-163833600	Weak transcription	Right Atrium	heart
15	chr6:163827400-163833800	Weak transcription	Aorta	Aorta
16	chr6:163827600-163832000	Weak transcription	HSMMtube	muscle
17	chr6:163827600-163833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:163827600-163833400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:163827600-163833400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:163827600-163833400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:163827600-163833400	Weak transcription	Fetal Lung	lung
22	chr6:163827600-163833400	Weak transcription	Fetal Stomach	stomach
23	chr6:163827600-163833400	Weak transcription	NHLF	lung
24	chr6:163827600-163833800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:163827800-163833400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:163827800-163833400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:163827800-163833400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:163827800-163833400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:163827800-163833400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:163828000-163833200	Weak transcription	HUVEC	blood vessel
31	chr6:163828000-163833600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:163828200-163832600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:163828200-163832600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:163828200-163833000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:163828200-163833400	Weak transcription	Liver	Liver
36	chr6:163828200-163833400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:163828200-163833400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:163828200-163833400	Weak transcription	Right Ventricle	heart
39	chr6:163828200-163833400	Weak transcription	GM12878-XiMat	blood
40	chr6:163828200-163833600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:163828400-163832000	Weak transcription	Brain Substantia Nigra	brain
42	chr6:163828600-163833000	Weak transcription	Adipose Nuclei	Adipose
43	chr6:163828800-163832000	Weak transcription	Brain Angular Gyrus	brain
44	chr6:163828800-163832000	Weak transcription	Fetal Heart	heart
45	chr6:163828800-163832200	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:163828800-163832200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:163828800-163832200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:163828800-163833200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:163828800-163833400	Weak transcription	NHDF-Ad	bronchial
50	chr6:163829000-163832400	Weak transcription	Primary monocytes fromperipheralblood	blood

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