Variant report

Variant	rs10915872
Chromosome Location	chr1:225949383-225949384
allele	G/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225948785..225952549-chr1:225953599..225956527,4	MCF-7	breast:
2	chr1:225942220..225946918-chr1:225947468..225951068,4	K562	blood:
3	chr1:225948184..225950809-chr1:225971310..225972848,2	K562	blood:
4	chr1:225840996..225843850-chr1:225947438..225950251,2	MCF-7	breast:
5	chr1:225947826..225950014-chr1:225953351..225955484,2	K562	blood:
6	chr1:225945507..225952186-chr1:225952608..225958481,10	MCF-7	breast:
7	chr1:225837871..225840623-chr1:225948803..225950378,2	MCF-7	breast:
8	chr1:225948046..225950619-chr1:225959798..225962169,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10915869	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10915871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915874	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915875	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12021669	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]
rs12021809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023140	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12023203	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023665	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs12025075	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12025085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12025267	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029847	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12031637	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032511	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12034342	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12038476	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12039184	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12042000	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12042778	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12044217	0.91[ASN][1000 genomes]
rs12047520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048472	1.00[YRI][hapmap]
rs12048908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562612	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1849685	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1857008	0.85[CEU][hapmap]
rs2078389	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[GIH][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3738035	1.00[AFR][1000 genomes]
rs3753650	1.00[AFR][1000 genomes]
rs4557929	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61849043	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61849046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61849047	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61851667	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6694856	0.83[TSI][hapmap]
rs716966	1.00[AFR][1000 genomes];0.89[EUR][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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225935000-225949600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:225939200-225949600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:225943400-225949400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:225943400-225949800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:225943400-225951800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:225943600-225949800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:225943600-225951400	Weak transcription	Pancreas	Pancrea
8	chr1:225943600-225951800	Weak transcription	Gastric	stomach
9	chr1:225943600-225954800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:225943800-225949800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:225943800-225951200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:225944000-225949400	Weak transcription	A549	lung
13	chr1:225944000-225949600	Weak transcription	Right Atrium	heart
14	chr1:225944200-225949400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:225944200-225949400	Weak transcription	NHLF	lung
16	chr1:225944200-225949600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:225944200-225949600	Weak transcription	HSMM	muscle
18	chr1:225944200-225951800	Weak transcription	Right Ventricle	heart
19	chr1:225944400-225949400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:225944400-225949600	Weak transcription	Left Ventricle	heart
21	chr1:225945600-225949800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:225946000-225949800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:225946000-225949800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:225946200-225949400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:225946200-225949800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:225946200-225949800	Weak transcription	Fetal Intestine Small	intestine
27	chr1:225946200-225959800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:225946400-225949600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:225946600-225949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:225946600-225949600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:225946600-225949600	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:225946600-225949600	Weak transcription	Fetal Thymus	thymus
33	chr1:225946600-225949600	Weak transcription	Ovary	ovary
34	chr1:225946600-225950200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:225946600-225951200	Weak transcription	Lung	lung
36	chr1:225946600-225951200	Weak transcription	Spleen	Spleen
37	chr1:225946600-225955400	Weak transcription	Fetal Intestine Large	intestine
38	chr1:225947000-225949600	Weak transcription	Adipose Nuclei	Adipose
39	chr1:225947000-225949600	Weak transcription	Fetal Lung	lung
40	chr1:225948200-225949400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:225948600-225949600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:225948600-225949600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:225948600-225950400	Weak transcription	Aorta	Aorta
44	chr1:225948800-225949400	Enhancers	NHDF-Ad	bronchial
45	chr1:225948800-225952200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:225949200-225949600	Enhancers	NH-A	brain
47	chr1:225949200-225950200	Enhancers	HepG2	liver
48	chr1:225949200-225951400	Enhancers	Osteobl	bone

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