Variant report

Variant	rs10861339
Chromosome Location	chr12:105453269-105453270
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105452142..105453731-chr12:105456982..105459077,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1014502	0.81[CEU][hapmap]
rs10459164	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861359	0.81[CEU][hapmap]
rs10861361	0.81[CEU][hapmap]
rs11112355	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112360	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112363	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112364	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112370	0.81[CEU][hapmap]
rs11112376	0.81[CEU][hapmap]
rs11112412	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs11112416	0.81[CEU][hapmap]
rs11112421	0.81[CEU][hapmap]
rs11112432	0.81[CEU][hapmap]
rs11831854	0.81[CEU][hapmap]
rs12228093	0.83[CEU][hapmap]
rs12230762	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12823614	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317955	0.81[CEU][hapmap]
rs1373552	0.81[CEU][hapmap]
rs1444611	0.81[CEU][hapmap]
rs17036625	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272495	0.81[CEU][hapmap]
rs2293643	0.81[CEU][hapmap]
rs2293644	0.81[CEU][hapmap]
rs34119882	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34384505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34891908	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35073181	0.83[EUR][1000 genomes]
rs35132501	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794223	0.80[CEU][hapmap]
rs3794227	0.87[CEU][hapmap]
rs3817607	0.81[CEU][hapmap]
rs4964121	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs4964336	0.81[CEU][hapmap]
rs755604	0.81[CEU][hapmap]
rs8015	0.82[CEU][hapmap]
rs881279	0.81[CEU][hapmap]

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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105409400-105465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr12:105413000-105476800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:105413200-105457800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:105414800-105454000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:105420000-105477000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:105423200-105459400	Weak transcription	Lung	lung
7	chr12:105431400-105461600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:105431800-105454800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:105432200-105454600	Weak transcription	NHEK	skin
10	chr12:105435200-105453600	Weak transcription	Fetal Stomach	stomach
11	chr12:105435600-105467400	Weak transcription	Brain Substantia Nigra	brain
12	chr12:105441200-105477000	Weak transcription	Gastric	stomach
13	chr12:105441400-105453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:105441400-105454800	Weak transcription	Pancreas	Pancrea
15	chr12:105441600-105458200	Weak transcription	Right Ventricle	heart
16	chr12:105442400-105469800	Weak transcription	Fetal Lung	lung
17	chr12:105443400-105465000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:105444000-105453600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:105445800-105472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:105447000-105461600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:105447000-105464600	Weak transcription	Left Ventricle	heart
22	chr12:105447000-105468000	Weak transcription	K562	blood
23	chr12:105447000-105468600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:105447200-105462000	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:105447200-105466800	Weak transcription	Brain Angular Gyrus	brain
26	chr12:105447200-105477200	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:105447400-105454600	Weak transcription	Adipose Nuclei	Adipose
28	chr12:105447400-105458200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:105448200-105461400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:105448800-105454800	Strong transcription	HMEC	breast
31	chr12:105448800-105459800	Weak transcription	Ovary	ovary
32	chr12:105448800-105461200	Strong transcription	Osteobl	bone
33	chr12:105449000-105455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:105449000-105456800	Strong transcription	HSMM	muscle
35	chr12:105449200-105454800	Weak transcription	Aorta	Aorta
36	chr12:105449400-105476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:105449800-105454200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:105450200-105456800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:105450400-105456800	Strong transcription	NH-A	brain
40	chr12:105450600-105454600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:105450600-105461400	Strong transcription	HSMMtube	muscle
42	chr12:105450600-105461800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:105450800-105456800	Strong transcription	Brain Germinal Matrix	brain
44	chr12:105450800-105461400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:105450800-105468200	Weak transcription	Brain Anterior Caudate	brain
46	chr12:105451200-105455200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:105451200-105457000	Strong transcription	NHLF	lung
48	chr12:105451400-105454800	Weak transcription	Fetal Brain Male	brain
49	chr12:105451400-105458600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:105451600-105457000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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