Variant report

Variant	rs2292682
Chromosome Location	chr12:104156520-104156521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10861094	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10861095	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861096	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861097	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861104	0.84[ASN][1000 genomes]
rs11111750	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111752	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111754	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11111755	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11111757	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111758	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111759	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111762	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111763	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111765	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11111767	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11111771	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11111776	0.83[EUR][1000 genomes]
rs11111778	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11111779	0.80[EUR][1000 genomes]
rs1565773	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs15918	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866292	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1976256	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751204	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812805	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964298	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964823	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4964827	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964830	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4981032	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4981036	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751448	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869993	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9132	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs934847	0.80[EUR][1000 genomes]
rs954920	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899486	chr12:104118587-104170474	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2292682	RP11-341G23.4	cis	Thyroid	GTEx
rs2292682	RP11-341G23.4	cis	Esophagus Muscularis	GTEx
rs2292682	RP11-341G23.4	cis	Muscle Skeletal	GTEx
rs2292682	RP11-341G23.4	cis	Artery Aorta	GTEx
rs2292682	RP11-341G23.4	cis	Artery Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104145800-104166800	Weak transcription	Right Atrium	heart
2	chr12:104146200-104169400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:104147000-104159600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:104147000-104165400	Strong transcription	Stomach Smooth Muscle	stomach
5	chr12:104149000-104156800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:104150000-104156600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:104150000-104166800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:104151400-104158000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:104151600-104170400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:104152000-104159800	Weak transcription	Lung	lung
11	chr12:104152400-104159400	Weak transcription	Gastric	stomach
12	chr12:104152400-104160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:104152400-104162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:104152400-104162800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:104152600-104158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:104152600-104160600	Strong transcription	Spleen	Spleen
17	chr12:104152600-104161600	Strong transcription	HMEC	breast
18	chr12:104152600-104162600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:104152600-104162600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:104152600-104162800	Weak transcription	Psoas Muscle	Psoas
21	chr12:104152600-104171200	Weak transcription	Esophagus	oesophagus
22	chr12:104152800-104159000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:104152800-104159200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:104152800-104159600	Weak transcription	Fetal Muscle Leg	muscle
25	chr12:104152800-104162800	Weak transcription	Brain Angular Gyrus	brain
26	chr12:104152800-104165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:104153200-104162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:104153800-104161600	Strong transcription	Liver	Liver
30	chr12:104154200-104157200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:104154200-104157600	Strong transcription	Rectal Smooth Muscle	rectum
32	chr12:104154200-104158400	Strong transcription	Placenta	Placenta
33	chr12:104154200-104161800	Strong transcription	Colon Smooth Muscle	Colon
34	chr12:104154400-104157600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:104154400-104159600	Weak transcription	Fetal Intestine Large	intestine
36	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:104154600-104157600	Strong transcription	HSMM	muscle
38	chr12:104154600-104158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:104154600-104160400	Strong transcription	NHEK	skin
40	chr12:104154600-104160600	Strong transcription	Aorta	Aorta
41	chr12:104154600-104160600	Strong transcription	Fetal Stomach	stomach
42	chr12:104154800-104157400	Strong transcription	HSMMtube	muscle
43	chr12:104154800-104157600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:104154800-104161400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:104154800-104161600	Strong transcription	NH-A	brain
46	chr12:104154800-104170600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:104155000-104161200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:104155000-104169000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:104155000-104170600	Weak transcription	Primary T cells from cord blood	blood
50	chr12:104155000-104170800	Weak transcription	Rectal Mucosa Donor 29	rectum

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