Variant report

Variant	rs1906198
Chromosome Location	chr2:62946658-62946659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62931680..62934441-chr2:62944780..62947311,3	K562	blood:
2	chr2:62936577..62938224-chr2:62946603..62948457,2	K562	blood:
3	chr2:62939404..62942481-chr2:62944890..62949579,4	K562	blood:
4	chr2:62931865..62934315-chr2:62945746..62950765,5	MCF-7	breast:
5	chr2:62920819..62922624-chr2:62945829..62948028,2	MCF-7	breast:
6	chr2:62931680..62936564-chr2:62937954..62947758,18	K562	blood:
7	chr2:62936577..62938663-chr2:62945664..62948457,3	K562	blood:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10153716	0.82[EUR][1000 genomes]
rs11682530	0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs11688816	0.92[JPT][hapmap]
rs11893131	0.83[CEU][hapmap]
rs12713467	0.81[EUR][1000 genomes]
rs12713468	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12989754	0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs13013218	0.92[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs1420018	0.86[JPT][hapmap]
rs1553832	0.87[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs17027429	0.88[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap]
rs1828398	0.88[CEU][hapmap]
rs189671	0.87[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2136737	0.87[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2215870	0.92[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.96[TSI][hapmap]
rs2421816	0.83[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs2430388	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap]
rs2539987	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs2710638	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs34104251	0.82[EUR][1000 genomes]
rs360797	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360799	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360800	0.83[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360801	0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360804	0.83[ASW][hapmap];0.83[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360807	0.87[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3927201	0.81[EUR][1000 genomes]
rs4461246	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4671050	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs4671450	0.82[EUR][1000 genomes]
rs6545971	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs6545972	0.88[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap]
rs6545973	0.83[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs7557501	0.88[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap]
rs7562149	0.92[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs7567923	0.88[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap]
rs7573756	0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs9678329	0.86[EUR][1000 genomes]
rs9973612	0.92[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62934200-62957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:62934200-62957800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:62934400-62957800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:62934600-62947400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:62934600-62951600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:62934600-62951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:62934600-62951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:62934600-62951800	Weak transcription	Esophagus	oesophagus
9	chr2:62934600-62951800	Weak transcription	Left Ventricle	heart
10	chr2:62934600-62952400	Weak transcription	Gastric	stomach
11	chr2:62934600-62957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:62934600-62957800	Weak transcription	Thymus	Thymus
13	chr2:62934600-62957800	Weak transcription	HSMMtube	muscle
14	chr2:62934800-62951800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:62935000-62948400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:62935200-62949000	Weak transcription	Fetal Intestine Large	intestine
17	chr2:62935800-62957800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:62936000-62951800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:62936200-62950200	Weak transcription	Brain Anterior Caudate	brain
20	chr2:62936200-62957800	Weak transcription	Small Intestine	intestine
21	chr2:62936400-62949800	Weak transcription	Fetal Lung	lung
22	chr2:62936400-62951400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:62936400-62951800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:62936400-62957800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:62936400-62957800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:62936600-62951800	Weak transcription	Pancreas	Pancrea
27	chr2:62936600-62957800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:62936600-62957800	Weak transcription	Hela-S3	cervix
29	chr2:62937200-62951400	Weak transcription	Fetal Heart	heart
30	chr2:62937200-62957800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:62937200-62957800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:62937400-62947200	Weak transcription	Primary T cells from cord blood	blood
33	chr2:62937400-62950000	Weak transcription	Primary B cells from cord blood	blood
34	chr2:62937400-62957800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:62938000-62951600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:62938600-62957800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:62938800-62950000	Weak transcription	Brain Germinal Matrix	brain
38	chr2:62939000-62949800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:62939400-62948200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:62939400-62949600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:62939400-62951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:62939400-62952200	Weak transcription	Fetal Brain Male	brain
43	chr2:62939600-62948400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:62939600-62949400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:62939600-62952400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:62939800-62952200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:62940000-62950200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:62940000-62952800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:62940400-62950000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:62941400-62948400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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