Variant report

Variant	rs7974089
Chromosome Location	chr12:32666561-32666562
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10506090	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10506093	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771960	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10771961	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771962	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10844222	0.82[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10844223	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844224	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10844226	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844227	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844228	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844229	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844230	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844231	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844232	0.91[ASN][1000 genomes]
rs10844234	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052040	0.91[ASN][1000 genomes]
rs11052041	0.94[ASN][1000 genomes]
rs11052042	0.82[CEU][hapmap];0.89[ASN][1000 genomes]
rs11052046	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052052	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11052053	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11608343	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366886	0.91[ASN][1000 genomes]
rs1500875	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1500876	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17536908	0.91[ASN][1000 genomes]
rs2036266	0.83[ASN][1000 genomes]
rs2133943	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2133944	0.91[ASN][1000 genomes]
rs4105685	0.96[ASN][1000 genomes]
rs4520681	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61928965	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7308163	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73092002	0.96[ASN][1000 genomes]
rs73094103	0.96[ASN][1000 genomes]
rs7953022	0.91[ASN][1000 genomes]
rs7962342	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7964715	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967306	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967702	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970857	0.91[ASN][1000 genomes]
rs7977101	0.91[ASN][1000 genomes]
rs7980242	0.80[CEU][hapmap]
rs7980571	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32655200-32686000	Weak transcription	Lung	lung
2	chr12:32656000-32668000	Weak transcription	Fetal Thymus	thymus
3	chr12:32656200-32668000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:32656400-32685800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:32658600-32667800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:32658600-32682000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:32659400-32667000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:32659600-32668000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:32659600-32675200	Weak transcription	Fetal Stomach	stomach
10	chr12:32659800-32669000	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:32661000-32668000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:32661000-32668000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:32661200-32668200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:32661200-32675600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:32661400-32668200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:32661400-32668800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:32661600-32668000	Weak transcription	HUVEC	blood vessel
18	chr12:32661800-32667800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:32661800-32668000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:32661800-32668200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr12:32661800-32674000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:32661800-32674000	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:32662000-32668200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:32662000-32671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:32662000-32674800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:32662000-32675600	Weak transcription	Fetal Brain Male	brain
27	chr12:32662800-32667800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:32663000-32668000	Weak transcription	Ovary	ovary
29	chr12:32663000-32669200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:32663000-32674600	Weak transcription	Brain Angular Gyrus	brain
31	chr12:32663200-32668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:32663200-32668000	Weak transcription	Stomach Mucosa	stomach
33	chr12:32663200-32668200	Weak transcription	Brain Substantia Nigra	brain
34	chr12:32663200-32673800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:32665000-32666600	Enhancers	Fetal Intestine Large	intestine
36	chr12:32665000-32666600	Enhancers	Fetal Intestine Small	intestine
37	chr12:32665000-32666800	Enhancers	Psoas Muscle	Psoas
38	chr12:32665200-32666600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr12:32665200-32666800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:32665400-32666600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:32665400-32666600	Enhancers	Gastric	stomach
42	chr12:32665400-32666600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr12:32665400-32666800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr12:32665400-32670000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:32665600-32666600	Enhancers	Liver	Liver
46	chr12:32665800-32667800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:32665800-32668000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:32665800-32675600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:32666000-32666600	Enhancers	Pancreas	Pancrea
50	chr12:32666000-32666800	Enhancers	Duodenum Smooth Muscle	Duodenum

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