Variant report

Variant	rs10444553
Chromosome Location	chr12:39294076-39294077
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39294074..39295589-chr12:39295957..39298877,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10161183	0.90[ASN][1000 genomes]
rs10876208	0.96[AMR][1000 genomes];0.98[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];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11835596	0.85[YRI][hapmap]
rs1400280	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1400285	0.96[AMR][1000 genomes];0.95[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];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1516558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[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];0.82[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	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2388172	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]
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];0.82[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];0.92[ASN][1000 genomes]
rs4595586	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768388	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56149694	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56344858	0.86[ASN][1000 genomes]
rs6580849	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[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];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7970097	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[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:42 , 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	chr12:39285000-39296400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:39286000-39294600	Weak transcription	Lung	lung
4	chr12:39286600-39297400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:39287400-39296400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:39287400-39298600	Weak transcription	Aorta	Aorta
7	chr12:39288000-39296600	Weak transcription	Liver	Liver
8	chr12:39289600-39297000	Weak transcription	HUVEC	blood vessel
9	chr12:39290200-39297600	Weak transcription	Adipose Nuclei	Adipose
10	chr12:39290400-39296200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:39290600-39297000	Weak transcription	Right Atrium	heart
12	chr12:39290800-39297600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:39290800-39298600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:39291000-39294200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:39292000-39294200	Active TSS	GM12878-XiMat	blood
16	chr12:39292200-39295400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:39292200-39295400	Weak transcription	Hela-S3	cervix
18	chr12:39292200-39296400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:39292200-39297200	Weak transcription	Placenta	Placenta
20	chr12:39292400-39297000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:39292400-39297200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:39292400-39297400	Weak transcription	HMEC	breast
23	chr12:39292400-39297600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:39292400-39297600	Weak transcription	NHDF-Ad	bronchial
25	chr12:39292400-39298800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:39292600-39296800	Weak transcription	NHEK	skin
27	chr12:39292600-39297000	Weak transcription	A549	lung
28	chr12:39292800-39297000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:39292800-39297000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:39292800-39297600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:39292800-39297600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:39292800-39298000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:39293000-39297400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:39293000-39297600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:39293000-39298400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:39293200-39296400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:39293200-39297000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:39293200-39297200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:39293200-39297400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:39293400-39297000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:39293600-39297000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:39293800-39294200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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