Variant report

Variant	rs11172184
Chromosome Location	chr12:57763520-57763521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57762333..57763849-chr12:57764785..57767656,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11172139	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs11172145	0.86[AMR][1000 genomes]
rs11172152	0.88[AMR][1000 genomes]
rs11172161	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11172163	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11172166	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172169	0.81[AMR][1000 genomes]
rs11172176	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11172177	0.81[AMR][1000 genomes]
rs11172190	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs11172197	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11172212	0.81[EUR][1000 genomes]
rs12812140	0.80[AMR][1000 genomes]
rs34095989	1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs34453452	0.90[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34537746	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35058761	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6581140	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67161907	0.85[EUR][1000 genomes]
rs7139302	0.87[AMR][1000 genomes]
rs7975026	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7975634	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv516655	chr12:57763520-57811414	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11172184	OR6C4	cis	parietal	SCAN
rs11172184	DKFZP586D0919	cis	multi-tissue	Pritchard

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57694000-57780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:57695200-57794600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:57704400-57789200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:57722000-57765200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:57722800-57771200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:57722800-57786200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:57727200-57764400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:57728000-57766600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:57731400-57789800	Weak transcription	Small Intestine	intestine
10	chr12:57731600-57796000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:57732800-57771800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr12:57734200-57779400	Weak transcription	Spleen	Spleen
13	chr12:57735200-57764400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:57736400-57765600	Weak transcription	Ovary	ovary
15	chr12:57736400-57784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:57736400-57795000	Weak transcription	Right Ventricle	heart
17	chr12:57736600-57782000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:57736600-57782400	Weak transcription	HSMM	muscle
19	chr12:57736600-57782800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:57736800-57764400	Weak transcription	HSMMtube	muscle
21	chr12:57736800-57766000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:57740400-57784000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:57741200-57765000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:57741200-57782800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:57742400-57785800	Weak transcription	Fetal Brain Female	brain
26	chr12:57745000-57787800	Weak transcription	Placenta	Placenta
27	chr12:57745200-57765600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:57745400-57772200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:57749400-57765400	Weak transcription	Brain Angular Gyrus	brain
30	chr12:57749800-57765400	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
32	chr12:57753600-57764600	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:57755800-57770000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:57756600-57771000	Weak transcription	K562	blood
35	chr12:57758800-57764600	Weak transcription	Osteobl	bone
36	chr12:57760200-57769800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:57760200-57769800	Weak transcription	Fetal Stomach	stomach
38	chr12:57760400-57764400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:57760400-57764400	Weak transcription	NHDF-Ad	bronchial
40	chr12:57760400-57769000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:57760400-57769800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:57760400-57775600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:57760600-57764200	Enhancers	Fetal Intestine Large	intestine
44	chr12:57760800-57763600	Enhancers	Fetal Intestine Small	intestine
45	chr12:57761000-57764600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr12:57761000-57766800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr12:57761000-57775800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:57761200-57765600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:57761200-57779400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:57761200-57787400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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