Variant report

Variant	rs4282557
Chromosome Location	chr8:59489542-59489543
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	chr8:59489367-59489603	K562	blood:	n/a	n/a
2	POLR2A	chr8:59489221-59489780	K562	blood:	n/a	n/a
3	POLR2A	chr8:59489257-59489664	K562	blood:	n/a	n/a
4	POLR2A	chr8:59489470-59489557	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr8:59484262-59500778	K562	blood:	n/a	n/a
6	POLR2A	chr8:59489304-59489775	A549	lung:	n/a	n/a
7	POLR2A	chr8:59488948-59489679	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr8:59489428-59489692	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:59488834..59491780-chr8:59497292..59499842,2	MCF-7	breast:
2	chr8:59482062..59484180-chr8:59488026..59489607,2	K562	blood:
3	chr8:59464704..59467459-chr8:59489336..59490887,2	MCF-7	breast:

Variant related genes	Relation type
SDCBP	TF binding region
ENSG00000137575	Chromatin interaction
ENSG00000035681	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10085973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10090425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10090964	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10092359	0.88[EUR][1000 genomes]
rs10094910	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10099153	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10099240	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10099912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10102709	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10104292	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10104568	0.81[JPT][hapmap]
rs10110111	0.84[EUR][1000 genomes]
rs10111052	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111506	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10113750	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10504256	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050488	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1050504	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11774558	0.81[EUR][1000 genomes]
rs11775194	0.83[CEU][hapmap]
rs11776003	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11782455	0.88[CEU][hapmap]
rs11783174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785141	0.81[EUR][1000 genomes]
rs12335008	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12543344	0.81[JPT][hapmap]
rs12674568	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12676593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12677290	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12680104	0.83[EUR][1000 genomes]
rs12680996	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1427162	0.81[JPT][hapmap]
rs1582824	0.81[JPT][hapmap]
rs16923562	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16923564	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16923588	0.88[EUR][1000 genomes]
rs17263989	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1976162	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1991359	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279460	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2279462	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2634527	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs28429491	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28650441	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28656336	0.90[EUR][1000 genomes]
rs28809811	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3739327	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808609	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs3816846	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4400366	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579515	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55774738	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56249776	0.81[EUR][1000 genomes]
rs59979442	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471729	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471731	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6981601	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6984439	0.81[JPT][hapmap]
rs6986129	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6987187	0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6995115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7009248	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7009374	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7011095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7014398	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72647434	0.89[EUR][1000 genomes]
rs72647435	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72647443	0.88[EUR][1000 genomes]
rs7817515	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7825996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7826122	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7826603	0.86[EUR][1000 genomes]
rs7827910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7840932	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7843989	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7844231	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs9297995	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9297996	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297997	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9297998	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297999	1.00[CEU][hapmap];0.90[EUR][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	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv890939	chr8:59471187-59544413	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1031537	chr8:59482949-59536971	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv397168	chr8:59488993-59497876	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59467400-59559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:59472800-59515800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:59473000-59493200	Weak transcription	Fetal Heart	heart
4	chr8:59473000-59493400	Weak transcription	Esophagus	oesophagus
5	chr8:59473000-59497400	Weak transcription	Stomach Mucosa	stomach
6	chr8:59473000-59506400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:59473200-59493400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:59473200-59508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr8:59473400-59492200	Weak transcription	Aorta	Aorta
10	chr8:59473400-59495400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr8:59474000-59497000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:59476600-59505600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr8:59476800-59490800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:59476800-59495400	Weak transcription	Pancreas	Pancrea
15	chr8:59476800-59500600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:59477000-59508200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:59477200-59489800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr8:59477200-59490600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr8:59477200-59490600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr8:59477200-59503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr8:59477200-59503400	Strong transcription	NHDF-Ad	bronchial
22	chr8:59477200-59506200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:59477600-59493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr8:59477600-59496800	Strong transcription	Placenta	Placenta
25	chr8:59477600-59500600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:59477600-59503600	Strong transcription	Osteobl	bone
27	chr8:59477600-59514200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:59477800-59508800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr8:59478000-59497000	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr8:59478000-59500400	Strong transcription	NH-A	brain
31	chr8:59478000-59500800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr8:59478000-59502800	Strong transcription	Fetal Thymus	thymus
33	chr8:59478000-59503000	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr8:59478000-59503200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr8:59478000-59506400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:59478000-59508200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr8:59478000-59508600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr8:59478000-59508800	Strong transcription	Fetal Intestine Large	intestine
39	chr8:59479000-59503800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr8:59479200-59499400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr8:59479200-59505600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:59479600-59500600	Strong transcription	HUVEC	blood vessel
43	chr8:59479600-59508000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr8:59480400-59503000	Strong transcription	Adipose Nuclei	Adipose
45	chr8:59480600-59515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr8:59481200-59498000	Weak transcription	Brain Substantia Nigra	brain
47	chr8:59481400-59502000	Weak transcription	Fetal Brain Male	brain
48	chr8:59482000-59493400	Weak transcription	Right Ventricle	heart
49	chr8:59482200-59492200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr8:59482200-59492200	Weak transcription	Lung	lung

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