Variant report

Variant	rs1259409
Chromosome Location	chr12:31716743-31716744
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31715871..31718697-chr12:31719904..31722778,2	K562	blood:
2	chr12:31711892..31714332-chr12:31715777..31718020,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1012154	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs10771832	0.86[CHB][hapmap]
rs10843947	0.86[CHB][hapmap]
rs11051418	0.85[CHB][hapmap]
rs1150942	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs1150943	0.85[EUR][1000 genomes]
rs1150945	0.85[EUR][1000 genomes]
rs1150953	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs1150954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1150955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs11615961	0.86[CHB][hapmap]
rs1259233	0.84[EUR][1000 genomes]
rs1259235	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs1259353	0.85[EUR][1000 genomes]
rs1259354	0.83[EUR][1000 genomes]
rs1259356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1259395	0.82[EUR][1000 genomes]
rs1259405	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259426	0.82[ASN][1000 genomes]
rs1259430	0.87[CEU][hapmap]
rs1259435	0.82[EUR][1000 genomes]
rs1259437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1259438	0.86[EUR][1000 genomes]
rs1259441	0.86[EUR][1000 genomes]
rs1262390	0.85[EUR][1000 genomes]
rs1272773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1469673	0.86[CHB][hapmap]
rs1677186	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1677187	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1677189	0.86[CHB][hapmap]
rs1716216	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs2061761	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2116704	0.86[CHB][hapmap]
rs2374190	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs2568884	0.92[CHB][hapmap]
rs2568887	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs2604052	0.84[ASN][1000 genomes]
rs2617178	0.82[EUR][1000 genomes]
rs2617190	0.90[CHB][hapmap]
rs2617191	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2617200	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs2682695	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs2682697	0.83[CHB][hapmap]
rs3898368	0.85[CHB][hapmap]
rs708200	0.92[CHB][hapmap]
rs708209	0.86[CHB][hapmap]
rs708212	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs708217	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs7294574	0.86[CHB][hapmap]
rs7302698	0.86[CHB][hapmap]
rs792871	0.94[CEU][hapmap];0.82[CHB][hapmap]
rs793148	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs793150	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs793158	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs793161	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs793171	0.94[CEU][hapmap]
rs793173	0.82[EUR][1000 genomes]
rs793174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs793176	0.92[CHB][hapmap]
rs793177	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs793186	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs793191	0.94[CEU][hapmap];0.84[CHB][hapmap]
rs7959877	0.86[CHB][hapmap]
rs7962896	0.86[CHB][hapmap]
rs7975761	0.86[CHB][hapmap]
rs7976644	0.86[CHB][hapmap]
rs899159	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs976874	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31696200-31722400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:31709200-31727600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:31709400-31722600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:31710200-31723800	Weak transcription	Pancreas	Pancrea
5	chr12:31711000-31727400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:31712200-31721000	Weak transcription	Primary B cells from cord blood	blood
7	chr12:31712200-31723600	Weak transcription	NH-A	brain
8	chr12:31713600-31720800	Weak transcription	Aorta	Aorta
9	chr12:31713800-31720200	Weak transcription	Fetal Intestine Small	intestine
10	chr12:31714000-31721400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:31714200-31726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:31714200-31728600	Weak transcription	Psoas Muscle	Psoas
13	chr12:31714400-31717600	Weak transcription	Ovary	ovary
14	chr12:31714400-31720600	Weak transcription	HepG2	liver
15	chr12:31714400-31721400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:31715200-31719600	Weak transcription	A549	lung
17	chr12:31715600-31716800	Weak transcription	Left Ventricle	heart
18	chr12:31715800-31723600	Weak transcription	Fetal Brain Female	brain
19	chr12:31716200-31716800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:31716200-31723600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:31716200-31723600	Weak transcription	Fetal Heart	heart
22	chr12:31716400-31718200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:31716400-31721400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:31716400-31723600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:31716600-31721400	Enhancers	GM12878-XiMat	blood
26	chr12:31716600-31724000	Weak transcription	Gastric	stomach

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