Variant report

Variant	rs10205625
Chromosome Location	chr2:142887869-142887870
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173835516..173837699-chr2:142887430..142889764,2	MCF-7	breast:
2	chr2:97534313..97536042-chr2:142885468..142888404,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000168758	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10188131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328304	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328797	0.87[AMR][1000 genomes]
rs13422148	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430169	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856855	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59636122	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963462	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963463	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9653181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv979390	chr2:142883251-142888150	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142885400-142890800	Active TSS	Brain Anterior Caudate	brain
2	chr2:142885600-142890400	Active TSS	Brain Substantia Nigra	brain
3	chr2:142885800-142889800	Active TSS	Brain Angular Gyrus	brain
4	chr2:142885800-142890000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr2:142886000-142890000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:142887200-142889000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:142887200-142889800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:142887400-142888000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr2:142887400-142888000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
10	chr2:142887400-142888000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
11	chr2:142887400-142888000	Flanking Active TSS	Hela-S3	cervix
12	chr2:142887400-142888200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:142887400-142888200	Flanking Active TSS	Liver	Liver
14	chr2:142887400-142888200	Active TSS	Pancreas	Pancrea
15	chr2:142887400-142888400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:142887400-142888600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:142887400-142888600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr2:142887400-142888800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:142887400-142889200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:142887400-142889200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:142887400-142889200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:142887400-142889400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr2:142887400-142889400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:142887400-142889400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:142887400-142889400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr2:142887400-142889400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr2:142887400-142889600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:142887400-142889600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:142887400-142889600	Active TSS	Right Atrium	heart
30	chr2:142887600-142888000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:142887600-142888000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:142887600-142888000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
33	chr2:142887600-142888000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:142887600-142888000	Bivalent Enhancer	Placenta	Placenta
35	chr2:142887600-142888000	Bivalent Enhancer	Left Ventricle	heart
36	chr2:142887600-142888000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
37	chr2:142887600-142888000	Flanking Active TSS	NH-A	brain
38	chr2:142887600-142888000	Bivalent/Poised TSS	NHDF-Ad	bronchial
39	chr2:142887600-142888200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:142887600-142888200	Flanking Active TSS	Fetal Brain Female	brain
41	chr2:142887600-142888200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
42	chr2:142887600-142888200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
43	chr2:142887600-142888400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:142887600-142888400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr2:142887600-142888600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr2:142887600-142888600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr2:142887600-142888600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
48	chr2:142887600-142888600	Flanking Active TSS	Right Ventricle	heart
49	chr2:142887600-142889000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:142887600-142889000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon

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