Variant report

Variant	rs12249709
Chromosome Location	chr10:96067595-96067596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96065535..96067850-chr10:96072045..96074764,2	K562	blood:
2	chr10:96066295..96067881-chr10:96069190..96071900,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11187855	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187896	1.00[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11187898	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs11187903	1.00[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs11187904	1.00[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs11187954	1.00[AMR][1000 genomes]
rs11188002	1.00[AMR][1000 genomes]
rs12243492	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12243849	0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12249578	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs12250011	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250480	1.00[AMR][1000 genomes]
rs12254178	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12254730	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256637	1.00[AMR][1000 genomes]
rs12259382	0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12259622	0.82[YRI][hapmap]
rs12266679	1.00[AMR][1000 genomes]
rs12266908	0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12269029	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2244404	1.00[AMR][1000 genomes]
rs57412910	1.00[AMR][1000 genomes]
rs60996053	1.00[AMR][1000 genomes]
rs61751499	1.00[EUR][1000 genomes]
rs6583938	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067896	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs7081603	1.00[AMR][1000 genomes]
rs7082254	1.00[AMR][1000 genomes]
rs7092351	1.00[EUR][1000 genomes]
rs73319896	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73319898	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73321857	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73323523	1.00[AMR][1000 genomes]
rs73323528	1.00[AMR][1000 genomes]
rs73327452	1.00[AMR][1000 genomes]
rs73327462	1.00[AMR][1000 genomes]
rs73327472	1.00[AMR][1000 genomes]
rs73327486	1.00[AMR][1000 genomes]
rs73327491	1.00[AMR][1000 genomes]
rs73327495	1.00[AMR][1000 genomes]
rs73329611	1.00[AMR][1000 genomes]
rs7907525	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911571	1.00[CHD][hapmap]
rs9665608	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96015000-96070200	Weak transcription	Fetal Brain Female	brain
2	chr10:96031800-96121000	Weak transcription	Stomach Mucosa	stomach
3	chr10:96036000-96081600	Weak transcription	Left Ventricle	heart
4	chr10:96037800-96069000	Weak transcription	Gastric	stomach
5	chr10:96043600-96121000	Weak transcription	Psoas Muscle	Psoas
6	chr10:96047800-96068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:96048800-96074800	Weak transcription	Placenta	Placenta
8	chr10:96049400-96081600	Weak transcription	Spleen	Spleen
9	chr10:96052800-96073600	Weak transcription	Ovary	ovary
10	chr10:96053000-96068200	Weak transcription	Fetal Brain Male	brain
11	chr10:96053000-96083200	Weak transcription	Fetal Kidney	kidney
12	chr10:96053200-96081600	Weak transcription	Brain Substantia Nigra	brain
13	chr10:96053400-96069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr10:96053400-96073000	Weak transcription	Fetal Lung	lung
15	chr10:96055200-96074600	Strong transcription	Fetal Muscle Leg	muscle
16	chr10:96059000-96074800	Weak transcription	Adipose Nuclei	Adipose
17	chr10:96059400-96083200	Weak transcription	Brain Anterior Caudate	brain
18	chr10:96059600-96081600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:96059800-96067800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:96060000-96074800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:96063200-96068200	Weak transcription	Colonic Mucosa	Colon
22	chr10:96063600-96076600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr10:96064200-96070600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr10:96064400-96068600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr10:96064400-96069400	Strong transcription	Fetal Intestine Large	intestine
26	chr10:96064400-96073800	Strong transcription	Fetal Stomach	stomach
27	chr10:96064600-96069000	Weak transcription	HepG2	liver
28	chr10:96064600-96069800	Strong transcription	Fetal Intestine Small	intestine
29	chr10:96064800-96070000	Weak transcription	Liver	Liver
30	chr10:96064800-96071600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr10:96064800-96072600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:96066000-96067600	Strong transcription	Aorta	Aorta
33	chr10:96066000-96074800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr10:96066200-96067800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr10:96066200-96071000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr10:96066200-96071800	Strong transcription	HSMMtube	muscle
37	chr10:96066200-96074800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr10:96066400-96070400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:96066400-96075200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr10:96067000-96067800	Weak transcription	A549	lung
41	chr10:96067200-96067600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:96067200-96067600	Enhancers	HUVEC	blood vessel
43	chr10:96067200-96068800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:96067200-96074800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:96067200-96075000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr10:96067400-96074800	Weak transcription	Pancreas	Pancrea
47	chr10:96067400-96081800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr10:96067400-96084400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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