Variant report

Variant	rs12138458
Chromosome Location	chr1:62174728-62174729
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:62173080..62176930-chr1:62205875..62209587,4	MCF-7	breast:
2	chr1:62173473..62177807-chr1:62188633..62191997,6	K562	blood:
3	chr1:62172595..62175082-chr1:62181867..62184619,2	K562	blood:
4	chr1:62172803..62176394-chr1:62188013..62191041,5	K562	blood:

Variant related genes	Relation type
ENSG00000271200	Chromatin interaction
ENSG00000132849	Chromatin interaction
ENSG00000162604	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11207805	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11207809	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207818	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11207819	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12125602	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12125626	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12144281	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1463777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2047276	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2172957	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4915771	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4915773	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56143974	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544580	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
2	chr1:62140000-62189000	Weak transcription	NHLF	lung
3	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:62146200-62190200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:62152400-62175200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:62158600-62189800	Weak transcription	Pancreas	Pancrea
7	chr1:62161200-62180600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:62161800-62179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:62162600-62177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:62163400-62181800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:62163800-62174800	Weak transcription	Hela-S3	cervix
12	chr1:62165000-62175800	Weak transcription	Right Atrium	heart
13	chr1:62165000-62189800	Weak transcription	Aorta	Aorta
14	chr1:62165400-62189400	Weak transcription	Fetal Brain Male	brain
15	chr1:62165400-62189600	Weak transcription	Right Ventricle	heart
16	chr1:62165400-62189800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:62166400-62176600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:62166400-62176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:62166400-62189400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:62166600-62187400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:62166600-62189400	Weak transcription	A549	lung
22	chr1:62166800-62178000	Weak transcription	Brain Angular Gyrus	brain
23	chr1:62166800-62189400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:62167600-62175200	Strong transcription	Fetal Stomach	stomach
25	chr1:62167600-62177200	Weak transcription	Brain Substantia Nigra	brain
26	chr1:62168400-62177600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:62169000-62176000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr1:62169600-62174800	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:62169600-62174800	Strong transcription	Thymus	Thymus
30	chr1:62169600-62175400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:62169600-62175400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:62169600-62177400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:62169600-62179400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:62169600-62179600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:62169600-62181200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:62169800-62175000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:62169800-62175200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:62169800-62175200	Strong transcription	Placenta	Placenta
39	chr1:62169800-62175400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:62169800-62175400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:62169800-62175400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:62169800-62175800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:62169800-62176000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:62170000-62174800	Strong transcription	Primary B cells from cord blood	blood
45	chr1:62170000-62175000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:62170000-62175200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:62170000-62175600	Strong transcription	Fetal Thymus	thymus
48	chr1:62170000-62175800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:62170000-62175800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:62170000-62179200	Strong transcription	Primary monocytes fromperipheralblood	blood

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