Variant report

Variant	rs3002117
Chromosome Location	chr1:180772414-180772415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180752587..180754098-chr1:180771744..180774694,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10914096	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12085097	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118646	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1339768	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1970404	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2331626	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2331886	1.00[CEU][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2944259	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs2944262	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002113	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002115	0.90[EUR][1000 genomes]
rs3002116	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002123	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3013633	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3013634	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789366	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3843278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3845406	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3856058	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3897798	0.86[ASN][1000 genomes]
rs4083591	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs4108558	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4651073	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs66520411	0.90[EUR][1000 genomes]
rs6659049	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6659368	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6661105	0.86[CHB][hapmap]
rs6682974	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs67780680	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72707408	0.86[EUR][1000 genomes]
rs72723045	0.90[EUR][1000 genomes]
rs7514404	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7524547	0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541650	0.86[ASN][1000 genomes]
rs7548318	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs7550031	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9425881	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970145	0.86[CHB][hapmap]
rs9970363	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv3777	chr1:180741213-180780313	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180713000-180814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:180740800-180775600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:180741600-180784000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:180751400-180774600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:180754800-180781600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:180755000-180783800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:180755400-180775800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:180755400-180803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:180755400-180820400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:180755600-180774200	Weak transcription	Dnd41	blood
11	chr1:180755600-180775200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:180755800-180777800	Weak transcription	Fetal Brain Female	brain
13	chr1:180756000-180774600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:180756000-180781400	Weak transcription	Liver	Liver
15	chr1:180756800-180778800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:180756800-180810200	Weak transcription	Fetal Brain Male	brain
17	chr1:180757400-180779400	Weak transcription	Left Ventricle	heart
18	chr1:180758000-180804000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:180758600-180774400	Weak transcription	K562	blood
20	chr1:180758600-180781200	Weak transcription	Adipose Nuclei	Adipose
21	chr1:180758800-180772600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:180759000-180775400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:180759000-180776800	Weak transcription	Primary T cells from cord blood	blood
24	chr1:180759000-180794800	Weak transcription	Fetal Intestine Small	intestine
25	chr1:180759200-180772600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:180759200-180774600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:180759200-180774600	Weak transcription	Primary B cells from cord blood	blood
28	chr1:180759400-180775200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:180759600-180775600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:180761200-180789200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:180761400-180772600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:180761400-180784400	Weak transcription	NHEK	skin
33	chr1:180761400-180794000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:180761400-180796400	Weak transcription	HMEC	breast
35	chr1:180761400-180804600	Weak transcription	Aorta	Aorta
36	chr1:180762000-180780600	Weak transcription	Osteobl	bone
37	chr1:180762000-180785200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:180762600-180775600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:180762800-180775400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:180763200-180775000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:180763200-180775200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:180763200-180780600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:180763600-180806800	Weak transcription	Psoas Muscle	Psoas
44	chr1:180763800-180780400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:180765000-180775200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:180766200-180784800	Weak transcription	Fetal Lung	lung
47	chr1:180766400-180773400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:180767400-180820400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:180767600-180795400	Weak transcription	Thymus	Thymus
50	chr1:180768000-180812000	Weak transcription	Pancreas	Pancrea

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