Variant report

Variant	rs2388172
Chromosome Location	chr12:39290539-39290540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39285246..39287445-chr12:39289748..39291988,2	K562	blood:
2	chr12:39268478..39271402-chr12:39288578..39290820,2	K562	blood:
3	chr12:39290114..39292966-chr12:39295688..39297919,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10161183	0.90[ASN][1000 genomes]
rs10444553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876208	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169482	0.90[JPT][hapmap]
rs11169518	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11169519	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169535	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11169616	0.91[ASN][1000 genomes]
rs11169760	0.87[ASN][1000 genomes]
rs11169768	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs11169807	0.92[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1400280	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1400285	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403521	0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1516558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523118	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1523121	0.87[ASN][1000 genomes]
rs1586373	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2138543	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34246358	0.85[ASN][1000 genomes]
rs35749392	0.89[ASN][1000 genomes]
rs3803020	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3887436	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4384412	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4595586	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4768388	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56149694	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56344858	0.86[ASN][1000 genomes]
rs6580849	1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7314227	0.96[ASN][1000 genomes]
rs7315271	0.90[JPT][hapmap]
rs7957376	0.90[JPT][hapmap]
rs7957999	0.81[ASN][1000 genomes]
rs7962363	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7970097	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39271800-39297200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:39285000-39291800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:39285000-39296400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:39286000-39294600	Weak transcription	Lung	lung
5	chr12:39286200-39291800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:39286200-39291800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:39286200-39291800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:39286400-39293600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:39286600-39297400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:39287200-39291800	Weak transcription	A549	lung
11	chr12:39287400-39291600	Weak transcription	Placenta	Placenta
12	chr12:39287400-39291800	Weak transcription	Hela-S3	cervix
13	chr12:39287400-39296400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:39287400-39298600	Weak transcription	Aorta	Aorta
15	chr12:39288000-39296600	Weak transcription	Liver	Liver
16	chr12:39288400-39291000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:39288600-39290600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:39288800-39290600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:39289600-39292000	Weak transcription	GM12878-XiMat	blood
20	chr12:39289600-39297000	Weak transcription	HUVEC	blood vessel
21	chr12:39289800-39291600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:39290000-39290800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr12:39290000-39290800	Enhancers	NHEK	skin
24	chr12:39290000-39291000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr12:39290000-39291200	Enhancers	Colon Smooth Muscle	Colon
26	chr12:39290200-39290600	Enhancers	Right Atrium	heart
27	chr12:39290200-39290600	Enhancers	HMEC	breast
28	chr12:39290200-39291200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr12:39290200-39291800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr12:39290200-39297600	Weak transcription	Adipose Nuclei	Adipose
31	chr12:39290400-39290800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr12:39290400-39293000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr12:39290400-39296200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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