Variant report

Variant	rs12562612
Chromosome Location	chr1:225958099-225958100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225834091..225845547-chr1:225952149..225961130,23	MCF-7	breast:
2	chr1:225956937..225960087-chr1:225960479..225963654,4	K562	blood:
3	chr1:225955657..225958331-chr1:225968298..225970381,2	K562	blood:
4	chr1:225957183..225958827-chr1:225960049..225962643,2	MCF-7	breast:
5	chr1:225952293..225956105-chr1:225956557..225960824,5	MCF-7	breast:
6	chr1:225956010..225958854-chr1:225963164..225966900,6	MCF-7	breast:
7	chr1:225952636..225956677-chr1:225957308..225960710,4	K562	blood:
8	chr1:225945507..225952186-chr1:225952608..225958481,10	MCF-7	breast:
9	chr1:225832104..225833710-chr1:225956622..225959260,2	MCF-7	breast:
10	chr1:225838129..225843793-chr1:225950745..225961465,25	MCF-7	breast:
11	chr1:225956759..225958408-chr1:225964562..225966540,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10915869	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10915871	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915872	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915874	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915875	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12021809	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12023203	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12023665	0.86[CEU][hapmap]
rs12025075	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12025085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12025267	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12026657	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029847	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12031637	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12032511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12034342	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038476	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12039184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042000	0.83[EUR][1000 genomes]
rs12042778	0.84[EUR][1000 genomes]
rs12047520	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12048908	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1849685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1857008	0.86[CEU][hapmap]
rs2078389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738035	1.00[AFR][1000 genomes]
rs3753650	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4557929	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61849043	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61849046	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61849047	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61851667	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs716966	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225946200-225959800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:225949600-225960400	Enhancers	Fetal Muscle Leg	muscle
3	chr1:225950600-225958200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:225952200-225960200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:225952200-225964400	Weak transcription	Fetal Brain Female	brain
6	chr1:225952200-225965600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:225953600-225958400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:225953600-225960000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225953600-225960200	Enhancers	Spleen	Spleen
10	chr1:225953800-225960200	Enhancers	Fetal Muscle Trunk	muscle
11	chr1:225954000-225960000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:225954200-225961000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:225954400-225958200	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:225954400-225960800	Enhancers	Fetal Stomach	stomach
15	chr1:225954400-225960800	Enhancers	Ovary	ovary
16	chr1:225954800-225964400	Weak transcription	Small Intestine	intestine
17	chr1:225955200-225960400	Enhancers	NHDF-Ad	bronchial
18	chr1:225955400-225960800	Enhancers	NHLF	lung
19	chr1:225955600-225958200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:225955600-225958800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:225955800-225958200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:225955800-225959800	Enhancers	Stomach Smooth Muscle	stomach
23	chr1:225955800-225960000	Enhancers	Fetal Lung	lung
24	chr1:225956000-225958200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:225956000-225958200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:225956000-225958200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:225956000-225958200	Weak transcription	Brain Angular Gyrus	brain
28	chr1:225956000-225958200	Weak transcription	Brain Anterior Caudate	brain
29	chr1:225956000-225958400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:225956000-225958600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:225956000-225959600	Weak transcription	Fetal Intestine Small	intestine
32	chr1:225956000-225959600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:225956000-225959600	Weak transcription	Stomach Mucosa	stomach
34	chr1:225956000-225960200	Weak transcription	Aorta	Aorta
35	chr1:225956200-225958400	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:225956200-225958400	Weak transcription	Fetal Intestine Large	intestine
37	chr1:225956200-225959600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:225956200-225959600	Weak transcription	Hela-S3	cervix
39	chr1:225956200-225959600	Weak transcription	HUVEC	blood vessel
40	chr1:225956200-225959800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:225956200-225960600	Weak transcription	HSMMtube	muscle
42	chr1:225956400-225958200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:225956400-225958200	Weak transcription	Adipose Nuclei	Adipose
44	chr1:225956400-225958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:225956400-225959600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:225956400-225959600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:225956400-225960200	Weak transcription	Colonic Mucosa	Colon
48	chr1:225956400-225960200	Weak transcription	Right Atrium	heart
49	chr1:225956600-225958600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:225956600-225958600	Weak transcription	Left Ventricle	heart

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