Variant report

Variant	rs829675
Chromosome Location	chr2:30710447-30710448
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	chr2:30704716..30706255-chr2:30708517..30710606,2	MCF-7	breast:
2	chr2:30703972..30706142-chr2:30708659..30711183,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10167083	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs10175399	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183928	0.85[JPT][hapmap]
rs12053428	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs12468064	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1252624	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1252625	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1252631	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1252646	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1252651	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1252654	1.00[JPT][hapmap]
rs1525062	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1869423	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1869424	0.86[CEU][hapmap]
rs1975555	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2121600	0.81[CEU][hapmap]
rs2123753	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2167969	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2177698	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2593442	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2593474	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs2602767	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2602808	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2609917	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2609945	0.82[JPT][hapmap]
rs2692035	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4952147	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6731031	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs6740440	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs6749074	0.81[EUR][1000 genomes]
rs7583211	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs7591110	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs7592355	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829563	0.82[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs829564	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829565	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829574	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829575	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829578	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829582	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829583	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829618	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829622	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829630	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829632	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829634	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829641	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829653	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829654	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829662	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829663	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829664	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829669	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829670	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829671	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829672	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829677	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829679	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829681	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829682	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs829684	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829695	0.85[JPT][hapmap]
rs829696	0.85[JPT][hapmap]
rs829699	0.85[JPT][hapmap]
rs844194	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs860487	1.00[JPT][hapmap]
rs866680	0.85[JPT][hapmap]
rs9309680	0.88[EUR][1000 genomes]

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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	32 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	chr2:30678600-30710600	Weak transcription	NHLF	lung
2	chr2:30696200-30710600	Weak transcription	Ovary	ovary
3	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
4	chr2:30698200-30710600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:30699000-30711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:30701200-30714400	Weak transcription	HSMM	muscle
7	chr2:30704600-30710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:30704600-30710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:30704600-30715800	Weak transcription	Psoas Muscle	Psoas
10	chr2:30704600-30719600	Weak transcription	Right Atrium	heart
11	chr2:30704600-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:30704600-30720600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:30704800-30710800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:30704800-30714200	Weak transcription	HSMMtube	muscle
15	chr2:30704800-30714400	Weak transcription	A549	lung
16	chr2:30705600-30710600	Weak transcription	Fetal Lung	lung
17	chr2:30705600-30711000	Weak transcription	Fetal Intestine Large	intestine
18	chr2:30705600-30711400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:30706000-30711000	Weak transcription	Small Intestine	intestine
20	chr2:30706400-30712200	Enhancers	Fetal Heart	heart
21	chr2:30707800-30710600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:30707800-30715200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:30708000-30715400	Weak transcription	Primary B cells from cord blood	blood
24	chr2:30708200-30710600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:30708200-30716000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:30709200-30710600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr2:30709200-30711800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:30709400-30711600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:30709400-30712000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:30709600-30710600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:30709600-30710600	Weak transcription	GM12878-XiMat	blood
32	chr2:30709600-30711600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr2:30709800-30710600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:30709800-30710600	Weak transcription	Left Ventricle	heart
35	chr2:30709800-30710600	Weak transcription	Osteobl	bone
36	chr2:30709800-30715800	Weak transcription	Right Ventricle	heart
37	chr2:30710000-30710600	Weak transcription	Pancreas	Pancrea
38	chr2:30710000-30710800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:30710200-30711600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:30710400-30710600	Enhancers	Colon Smooth Muscle	Colon
41	chr2:30710400-30711000	Enhancers	Primary T cells from cord blood	blood
42	chr2:30710400-30711400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:30710400-30711400	Enhancers	NHDF-Ad	bronchial
44	chr2:30710400-30711600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:30710400-30711600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:30710400-30711600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:30710400-30711600	Enhancers	Fetal Kidney	kidney
48	chr2:30710400-30711800	Enhancers	Duodenum Mucosa	Duodenum

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