Variant report

Variant	rs10173398
Chromosome Location	chr2:153354994-153354995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153353996..153356046-chr2:153357031..153359533,2	K562	blood:
2	chr2:153345928..153348906-chr2:153354040..153356962,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10166703	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10193625	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10195380	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10432494	0.92[ASN][1000 genomes]
rs11892232	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11892859	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11893683	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12614608	0.94[ASN][1000 genomes]
rs12617686	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623070	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12693378	0.83[CEU][hapmap]
rs2068886	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2346204	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2881336	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4471845	0.80[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4613221	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6434059	0.84[CEU][hapmap]
rs6434078	0.95[JPT][hapmap]
rs6721741	0.82[JPT][hapmap]
rs6736639	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6737006	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7425826	0.95[ASN][1000 genomes]
rs7590079	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288103	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153342600-153355800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:153343000-153360600	Enhancers	Brain Anterior Caudate	brain
3	chr2:153348600-153357200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:153348800-153370200	Weak transcription	Aorta	Aorta
5	chr2:153350400-153357400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:153350800-153355800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:153350800-153357000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:153350800-153360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:153351000-153355600	Weak transcription	Fetal Stomach	stomach
10	chr2:153351200-153355400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:153351400-153355200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:153351400-153355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:153351400-153357600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:153351400-153361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:153351600-153355200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:153351600-153359600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:153351800-153355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:153352000-153359800	Enhancers	Brain Substantia Nigra	brain
19	chr2:153352200-153356000	Enhancers	Brain Hippocampus Middle	brain
20	chr2:153352400-153355200	Weak transcription	Fetal Kidney	kidney
21	chr2:153353400-153356400	Enhancers	HepG2	liver
22	chr2:153353600-153355600	Weak transcription	Fetal Brain Male	brain
23	chr2:153353600-153357000	Enhancers	Hela-S3	cervix
24	chr2:153353800-153356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:153354000-153355800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:153354000-153356000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:153354200-153355000	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:153354200-153357200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr2:153354200-153357200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:153354200-153357200	Enhancers	Fetal Intestine Large	intestine
31	chr2:153354200-153357200	Enhancers	Fetal Intestine Small	intestine
32	chr2:153354200-153357200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:153354200-153358200	Enhancers	Adipose Nuclei	Adipose
34	chr2:153354200-153358800	Enhancers	Brain Angular Gyrus	brain
35	chr2:153354200-153360000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:153354400-153355400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:153354400-153355400	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr2:153354400-153356200	Enhancers	Colon Smooth Muscle	Colon
39	chr2:153354400-153356400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:153354400-153356600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:153354400-153361000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:153354600-153355200	Weak transcription	A549	lung
43	chr2:153354600-153355400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:153354600-153355400	Weak transcription	Psoas Muscle	Psoas
45	chr2:153354600-153355600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:153354600-153355600	Weak transcription	Colonic Mucosa	Colon
47	chr2:153354600-153355600	Weak transcription	Fetal Lung	lung
48	chr2:153354600-153355600	Weak transcription	Placenta	Placenta
49	chr2:153354600-153355600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:153354600-153355600	Weak transcription	Small Intestine	intestine

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