Variant report

Variant	rs10490472
Chromosome Location	chr2:53999774-53999775
allele	G/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	chr2:53999660-54000232	K562	blood:	n/a	n/a
2	CEBPB	chr2:53999760-53999976	A549	lung:	n/a	chr2:53999797-53999810 chr2:53999797-53999810

No.	Distal block	Cell Line	Cell type
1	chr2:53996518..54000180-chr2:54012874..54016675,4	K562	blood:
2	chr2:53993244..53996304-chr2:53997102..54000368,4	MCF-7	breast:
3	chr2:53998942..54000537-chr2:54013656..54015414,2	MCF-7	breast:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
ENSG00000143942	Chromatin interaction
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10204047	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10204432	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10490473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13387421	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13404007	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13426962	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17039534	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17045069	0.83[AMR][1000 genomes]
rs17045109	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045123	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17045139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17045239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17045241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17045286	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17045296	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2056650	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2287339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2287342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2287346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2287347	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs2302876	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2302880	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28834518	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3213768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3213774	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3755113	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3755114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815650	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3821079	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59951261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60972886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545368	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6724214	0.86[ASN][1000 genomes]
rs6761242	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72799242	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72799275	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72901302	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72902916	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72902923	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72902926	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72902929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7601553	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7605552	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs997643	0.83[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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53995400-54003600	Weak transcription	Small Intestine	intestine
2	chr2:53995600-54005800	Weak transcription	HSMM	muscle
3	chr2:53995600-54007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:53995600-54007400	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:53995600-54007800	Weak transcription	Placenta	Placenta
6	chr2:53995600-54008400	Weak transcription	Ovary	ovary
7	chr2:53995600-54009000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:53995600-54009000	Weak transcription	Lung	lung
9	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
11	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
13	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:53995800-54000600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:53995800-54000600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:53995800-54001000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:53995800-54001200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:53995800-54003000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:53995800-54006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:53995800-54008600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
23	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
24	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
25	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:53996000-54000800	Weak transcription	Fetal Intestine Large	intestine
29	chr2:53996000-54001200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:53996000-54004400	Weak transcription	Osteobl	bone
31	chr2:53996000-54005800	Weak transcription	Liver	Liver
32	chr2:53996000-54006800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:53996000-54009000	Weak transcription	Brain Substantia Nigra	brain
34	chr2:53996000-54011000	Weak transcription	Fetal Brain Male	brain
35	chr2:53996000-54011200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:53996000-54011600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:53996000-54011600	Weak transcription	Fetal Lung	lung
38	chr2:53996000-54011800	Weak transcription	NHDF-Ad	bronchial
39	chr2:53996200-54000600	Weak transcription	Fetal Stomach	stomach
40	chr2:53996200-54003000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:53996200-54003600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:53996200-54004400	Weak transcription	Primary B cells from cord blood	blood
43	chr2:53996200-54006400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:53996200-54006800	Weak transcription	NH-A	brain
45	chr2:53996200-54007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:53996200-54009800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:53996200-54011000	Weak transcription	Brain Angular Gyrus	brain
48	chr2:53996200-54011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:53996200-54012600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:53996400-54000600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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