Variant report

Variant	rs6473662
Chromosome Location	chr8:52808330-52808331
allele	A/C
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	CUX1	chr8:52808188-52808365	K562	blood:	n/a	n/a
2	POLR2A	chr8:52808235-52808351	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr8:52806101-52808455	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr8:52808230-52808374	ProgFib	skin:	n/a	n/a
5	POLR2A	chr8:52804446-52808348	K562	blood:	n/a	n/a
6	CTCF	chr8:52808193-52808392	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52807403..52809441-chr8:52809988..52811800,2	MCF-7	breast:
2	chr8:52762297..52765279-chr8:52806438..52808911,2	K562	blood:

Variant related genes	Relation type
ENSG00000228801	TF binding region
ENSG00000168300	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10106371	0.83[AMR][1000 genomes]
rs12164174	0.83[AMR][1000 genomes]
rs13255940	0.82[AFR][1000 genomes]
rs4321995	0.83[AMR][1000 genomes]
rs4401853	0.83[AMR][1000 genomes]
rs4518654	0.86[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap]
rs4545087	0.86[ASW][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[AMR][1000 genomes]
rs4607598	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4873614	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4873615	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4873620	0.83[AMR][1000 genomes]
rs6473664	0.83[AMR][1000 genomes]
rs7459831	0.83[AMR][1000 genomes]
rs7459885	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs7816619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7827030	0.83[AMR][1000 genomes]
rs9298468	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52771800-52810800	Weak transcription	Esophagus	oesophagus
2	chr8:52779400-52809000	Weak transcription	Fetal Kidney	kidney
3	chr8:52782200-52809600	Weak transcription	Aorta	Aorta
4	chr8:52797400-52809000	Weak transcription	HMEC	breast
5	chr8:52797400-52809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr8:52797400-52809600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:52797400-52810800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:52798000-52810800	Weak transcription	Spleen	Spleen
9	chr8:52798800-52808800	Weak transcription	Fetal Brain Female	brain
10	chr8:52799600-52809800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:52800000-52809000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr8:52801600-52810200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:52801800-52809600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:52801800-52810800	Weak transcription	Gastric	stomach
15	chr8:52802400-52810000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:52803400-52809800	Weak transcription	Colonic Mucosa	Colon
17	chr8:52803400-52810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:52804000-52809200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:52804000-52809400	Weak transcription	Fetal Muscle Leg	muscle
20	chr8:52804000-52809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:52804000-52809600	Weak transcription	Fetal Intestine Large	intestine
22	chr8:52804000-52809600	Weak transcription	Right Atrium	heart
23	chr8:52804200-52808600	Weak transcription	Pancreas	Pancrea
24	chr8:52804200-52809800	Weak transcription	Left Ventricle	heart
25	chr8:52804200-52810400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr8:52804200-52810400	Weak transcription	Lung	lung
27	chr8:52805000-52809200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:52805200-52809800	Weak transcription	Psoas Muscle	Psoas
29	chr8:52805800-52810000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr8:52806200-52808400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr8:52806200-52808400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr8:52806200-52809600	Enhancers	HepG2	liver
33	chr8:52806200-52810000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr8:52806400-52808400	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr8:52806400-52808400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr8:52806400-52808400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr8:52806400-52808400	Genic enhancers	K562	blood
38	chr8:52806400-52808600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr8:52806400-52808600	Enhancers	Colon Smooth Muscle	Colon
40	chr8:52806400-52808600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
41	chr8:52806400-52809200	Genic enhancers	Dnd41	blood
42	chr8:52806400-52809600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr8:52806400-52809800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr8:52806400-52809800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr8:52806400-52810200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr8:52806600-52808600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr8:52806600-52808600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr8:52806600-52810000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr8:52806600-52810000	Enhancers	Small Intestine	intestine
50	chr8:52806800-52808400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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