Variant report

Variant	rs1628871
Chromosome Location	chr12:42519688-42519689
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1069644	0.92[JPT][hapmap]
rs10880275	0.92[JPT][hapmap]
rs10880279	0.92[JPT][hapmap]
rs1226303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1238290	0.92[JPT][hapmap]
rs1463613	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1683198	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1683202	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1688854	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1688879	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1688884	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1732351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1732352	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3852592	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6582392	0.92[JPT][hapmap]
rs712106	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712119	0.92[JPT][hapmap]
rs712120	0.94[CEU][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs712122	0.92[JPT][hapmap]
rs712123	0.92[JPT][hapmap]
rs712125	0.92[JPT][hapmap]
rs712129	0.92[JPT][hapmap]
rs7303028	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7956016	0.92[JPT][hapmap]
rs7960176	0.92[JPT][hapmap]
rs7970115	0.85[JPT][hapmap]
rs7978993	0.91[JPT][hapmap]
rs824697	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs824716	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs824722	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs824724	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs824726	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs824734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs824736	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs824738	0.94[CEU][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs824741	0.92[JPT][hapmap]
rs844046	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs865420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
2	chr12:42476000-42524400	Weak transcription	Gastric	stomach
3	chr12:42476200-42524400	Weak transcription	Pancreas	Pancrea
4	chr12:42476600-42523800	Weak transcription	Hela-S3	cervix
5	chr12:42484400-42524800	Weak transcription	Right Ventricle	heart
6	chr12:42493000-42524400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:42493000-42534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:42505800-42522400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:42505800-42537000	Weak transcription	Fetal Stomach	stomach
10	chr12:42505800-42537000	Weak transcription	Lung	lung
11	chr12:42508400-42524600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:42512000-42522200	Weak transcription	HMEC	breast
13	chr12:42512000-42537400	Weak transcription	Ovary	ovary
14	chr12:42512400-42520800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:42512400-42521800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:42512400-42523800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:42512400-42523800	Weak transcription	HSMM	muscle
18	chr12:42512400-42537000	Weak transcription	Placenta	Placenta
19	chr12:42512600-42524400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:42512600-42524600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:42512800-42524400	Weak transcription	Left Ventricle	heart
22	chr12:42513000-42537000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr12:42513200-42523800	Weak transcription	NH-A	brain
24	chr12:42513200-42537200	Weak transcription	Primary T cells from cord blood	blood
25	chr12:42513600-42523800	Weak transcription	NHDF-Ad	bronchial
26	chr12:42513600-42523800	Weak transcription	NHLF	lung
27	chr12:42515400-42523600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:42518200-42519800	Enhancers	Liver	Liver
29	chr12:42518400-42519800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr12:42518400-42519800	Enhancers	Fetal Intestine Large	intestine
31	chr12:42518400-42521200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr12:42518600-42519800	Enhancers	Primary B cells from peripheral blood	blood
33	chr12:42518600-42519800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:42518600-42520200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:42518600-42520400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr12:42518600-42520400	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr12:42518600-42520800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:42518600-42522800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:42518800-42519800	Enhancers	Primary hematopoietic stem cells	blood
40	chr12:42518800-42520200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr12:42518800-42520400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:42519000-42519800	Enhancers	Primary B cells from cord blood	blood
43	chr12:42519000-42519800	Enhancers	GM12878-XiMat	blood
44	chr12:42519000-42520000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr12:42519000-42524800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:42519000-42537000	Weak transcription	Right Atrium	heart
47	chr12:42519200-42520200	Weak transcription	Brain Angular Gyrus	brain
48	chr12:42519200-42520400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr12:42519200-42520400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr12:42519200-42521200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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