Variant report

Variant	rs2168411
Chromosome Location	chr12:64431988-64431989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10444577	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10878102	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175238	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1162788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12228437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1344400	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378778	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1456046	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2647908	0.84[ASN][1000 genomes]
rs28366579	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4553444	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763134	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60987129	0.86[ASN][1000 genomes]
rs6581529	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963940	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980267	0.81[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs990309	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64380200-64433000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:64382800-64432800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:64415000-64432400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:64416600-64432400	Weak transcription	Fetal Brain Female	brain
5	chr12:64418600-64456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:64422800-64433200	Weak transcription	Small Intestine	intestine
7	chr12:64423000-64432600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:64423000-64433000	Weak transcription	HMEC	breast
9	chr12:64423400-64433000	Weak transcription	Fetal Stomach	stomach
10	chr12:64423400-64433000	Weak transcription	HSMMtube	muscle
11	chr12:64424600-64432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:64424800-64432400	Weak transcription	Stomach Mucosa	stomach
13	chr12:64424800-64432600	Weak transcription	NHLF	lung
14	chr12:64426200-64432600	Weak transcription	Brain Substantia Nigra	brain
15	chr12:64426400-64432400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:64426400-64432600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:64426400-64432600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:64426400-64433000	Weak transcription	Left Ventricle	heart
19	chr12:64428400-64433000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:64428800-64433400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:64428800-64450800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:64429000-64433000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:64429400-64432200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:64429400-64432400	Weak transcription	Brain Germinal Matrix	brain
25	chr12:64429400-64433200	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:64429600-64432600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:64429600-64433000	Weak transcription	Fetal Lung	lung
28	chr12:64429800-64432000	Enhancers	Pancreas	Pancrea
29	chr12:64430000-64432400	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:64430000-64432800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:64430000-64432800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:64430200-64432200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:64430200-64432400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:64430200-64433000	Weak transcription	Fetal Intestine Small	intestine
35	chr12:64430200-64433200	Weak transcription	Aorta	Aorta
36	chr12:64430200-64439800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:64430400-64433000	Weak transcription	HSMM	muscle
38	chr12:64430600-64432000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:64430600-64432400	Weak transcription	HUVEC	blood vessel
40	chr12:64430600-64432600	Weak transcription	Osteobl	bone
41	chr12:64430800-64433000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:64431000-64432800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:64431000-64432800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:64431200-64432000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:64431200-64432600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:64431200-64437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:64431400-64432200	Weak transcription	NHDF-Ad	bronchial
48	chr12:64431800-64432000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:64431800-64432600	Weak transcription	A549	lung
50	chr12:64431800-64432600	Weak transcription	NHEK	skin

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