Variant report

Variant	rs2010748
Chromosome Location	chr3:159509200-159509201
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159505829..159507763-chr3:159508214..159510388,2	K562	blood:
2	chr3:159506660..159510516-chr3:159511737..159514255,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCHIP1-1	chr3:159509172-159509448	uc_133_+
2	lnc-RP11-432B6.3.1-5	chr3:159509172-159509448	uc_133_-

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1009058	0.90[CEU][hapmap]
rs10936179	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490735	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491535	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1497762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs1675496	0.89[CEU][hapmap]
rs2169305	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs3851359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680524	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs56107912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270387	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270397	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6763138	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6780187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878736	0.82[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159493600-159509200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:159500400-159509200	Enhancers	HepG2	liver
4	chr3:159501800-159510200	Enhancers	Fetal Intestine Large	intestine
5	chr3:159502000-159522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:159503000-159510200	Enhancers	Fetal Intestine Small	intestine
7	chr3:159503800-159509600	Enhancers	Adipose Nuclei	Adipose
8	chr3:159504000-159518600	Enhancers	Brain Hippocampus Middle	brain
9	chr3:159504200-159518400	Enhancers	Brain Substantia Nigra	brain
10	chr3:159504600-159509400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:159504600-159511200	Enhancers	Brain Anterior Caudate	brain
12	chr3:159505000-159515000	Enhancers	Brain Angular Gyrus	brain
13	chr3:159505600-159512600	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:159505600-159515600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:159506000-159509200	Weak transcription	Lung	lung
16	chr3:159506000-159518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:159506200-159510000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:159506200-159522600	Weak transcription	Fetal Kidney	kidney
19	chr3:159506400-159509200	Weak transcription	Esophagus	oesophagus
20	chr3:159506400-159509200	Weak transcription	Left Ventricle	heart
21	chr3:159506400-159509200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr3:159506400-159509400	Weak transcription	Osteobl	bone
23	chr3:159506400-159511200	Enhancers	A549	lung
24	chr3:159506400-159512400	Weak transcription	Right Atrium	heart
25	chr3:159506400-159512600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:159506400-159513200	Weak transcription	NHLF	lung
27	chr3:159506400-159513800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:159506400-159522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:159506600-159514200	Weak transcription	Fetal Heart	heart
30	chr3:159506800-159513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:159507000-159509400	Weak transcription	HUVEC	blood vessel
32	chr3:159507000-159510200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:159507000-159512200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:159507000-159513600	Weak transcription	NH-A	brain
35	chr3:159507400-159512400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:159507400-159512600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:159507600-159509600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:159507600-159510200	Enhancers	Aorta	Aorta
39	chr3:159508000-159509200	Weak transcription	Small Intestine	intestine
40	chr3:159508000-159509400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:159508000-159513800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:159508000-159513800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:159508000-159514000	Weak transcription	HMEC	breast
44	chr3:159508200-159510600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:159508600-159509200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:159508600-159520600	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:159508800-159509200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:159508800-159509200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:159508800-159509200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:159508800-159509400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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