Variant report

Variant	rs10195380
Chromosome Location	chr2:153342552-153342553
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153326388..153330903-chr2:153339849..153343861,4	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10166703	0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10173398	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10193625	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10432494	0.94[ASN][1000 genomes]
rs11892232	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11892859	0.97[ASN][1000 genomes]
rs11893683	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12614608	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617686	0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623070	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2068886	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2346204	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2881336	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4471845	0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4613221	0.96[ASN][1000 genomes]
rs4664585	0.88[YRI][hapmap]
rs6434078	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6721741	0.82[JPT][hapmap]
rs6736639	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737006	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7425826	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7590079	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288103	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2830258	chr2:153318339-153349165	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153326200-153345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:153330800-153347400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:153334400-153353800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:153336000-153347600	Weak transcription	Aorta	Aorta
5	chr2:153338400-153345600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:153338400-153345800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:153338600-153346600	Weak transcription	Colonic Mucosa	Colon
8	chr2:153338600-153353400	Weak transcription	NHEK	skin
9	chr2:153339200-153342600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:153339400-153345600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:153340400-153346800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:153340600-153342800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:153340600-153345400	Weak transcription	Ovary	ovary
14	chr2:153340600-153347400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:153340600-153354200	Weak transcription	Small Intestine	intestine
16	chr2:153340800-153342800	Weak transcription	Fetal Lung	lung
17	chr2:153341000-153342600	Weak transcription	Pancreas	Pancrea
18	chr2:153341000-153345200	Weak transcription	Fetal Stomach	stomach
19	chr2:153341200-153345200	Weak transcription	Lung	lung
20	chr2:153341800-153343800	Enhancers	Fetal Intestine Large	intestine
21	chr2:153342000-153343400	Flanking Active TSS	HepG2	liver
22	chr2:153342000-153343600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:153342000-153343800	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:153342000-153344600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr2:153342000-153345800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:153342000-153349000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:153342000-153351600	Enhancers	Brain Substantia Nigra	brain
28	chr2:153342000-153351800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:153342200-153342600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr2:153342200-153342600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:153342200-153342800	Enhancers	Fetal Muscle Leg	muscle
32	chr2:153342200-153342800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:153342200-153343000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr2:153342200-153343000	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr2:153342200-153343000	Enhancers	Psoas Muscle	Psoas
36	chr2:153342200-153343200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:153342200-153343200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr2:153342200-153343200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr2:153342200-153343200	Enhancers	Colon Smooth Muscle	Colon
40	chr2:153342200-153343200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:153342200-153343400	Enhancers	Brain Angular Gyrus	brain
42	chr2:153342200-153343800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr2:153342200-153343800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:153342200-153343800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:153342200-153343800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:153342200-153343800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr2:153342200-153343800	Flanking Active TSS	A549	lung
48	chr2:153342200-153344000	Enhancers	Adipose Nuclei	Adipose
49	chr2:153342200-153344400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:153342400-153342600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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