Variant report

Variant	rs12473516
Chromosome Location	chr2:172840869-172840870
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	chr2:172837171..172840943-chr2:172841139..172845693,4	K562	blood:
2	chr2:172838818..172840890-chr2:172863304..172865043,2	K562	blood:

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10166352	0.80[ASN][1000 genomes]
rs10177679	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10179020	0.88[EUR][1000 genomes]
rs10188587	0.80[ASN][1000 genomes]
rs10196521	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1022358	0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap]
rs10432474	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10439296	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10930497	1.00[MEX][hapmap]
rs10930498	0.80[ASN][1000 genomes]
rs10930500	0.80[ASN][1000 genomes]
rs10930501	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105264	0.89[EUR][1000 genomes]
rs11676484	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677573	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs11683436	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11692418	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11695887	0.80[ASN][1000 genomes]
rs11903123	0.89[EUR][1000 genomes]
rs11903410	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467010	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12468218	0.80[ASN][1000 genomes]
rs12478215	0.80[ASN][1000 genomes]
rs12479374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12617265	0.88[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs12619137	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs12692979	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs13017988	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs13399316	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1400816	0.85[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs1443699	0.94[ASN][1000 genomes]
rs1443700	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1878583	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1982288	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996425	0.89[EUR][1000 genomes]
rs2028670	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028672	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2056202	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs2176466	0.82[JPT][hapmap]
rs2292813	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs2357064	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2357206	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs2357207	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357208	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28372952	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770443	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770444	0.89[EUR][1000 genomes]
rs3770453	0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap]
rs3770457	0.85[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs3791343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821092	0.85[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs3821094	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3821096	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4072279	0.80[ASN][1000 genomes]
rs4668417	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs59853867	0.80[ASN][1000 genomes]
rs60706248	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62182438	0.82[ASN][1000 genomes]
rs6433313	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6433315	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6433316	0.86[EUR][1000 genomes]
rs6433317	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs6433318	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433322	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6707142	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711813	0.81[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs6714214	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726050	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6733123	0.94[ASN][1000 genomes]
rs6736159	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs6740705	0.94[CHD][hapmap];0.83[GIH][hapmap];0.80[ASN][1000 genomes]
rs6742905	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753551	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6753859	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6757680	0.83[GIH][hapmap]
rs6758494	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6760680	0.82[JPT][hapmap]
rs718936	1.00[MEX][hapmap]
rs7340516	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7371503	1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs7371631	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560031	1.00[MEX][hapmap]
rs7579509	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7580132	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs7580232	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs7588025	0.82[JPT][hapmap]
rs7594478	0.86[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs7597525	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598232	0.90[ASN][1000 genomes]
rs925881	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs949548	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs970948	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv436276	chr2:172831435-172841517	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3458695	chr2:172832445-172841110	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3458694	chr2:172832493-172841085	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3458693	chr2:172832508-172841056	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3458697	chr2:172832579-172841009	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
4	chr2:172783600-172851000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:172796000-172855200	Weak transcription	Gastric	stomach
6	chr2:172807400-172845400	Weak transcription	Spleen	Spleen
7	chr2:172808000-172847200	Weak transcription	Fetal Brain Female	brain
8	chr2:172808000-172849400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:172811400-172846200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:172811800-172852200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:172811800-172855600	Weak transcription	Fetal Heart	heart
13	chr2:172812400-172845200	Weak transcription	Colonic Mucosa	Colon
14	chr2:172813000-172859200	Weak transcription	Fetal Brain Male	brain
15	chr2:172814000-172844400	Weak transcription	Pancreas	Pancrea
16	chr2:172815400-172850000	Weak transcription	HSMMtube	muscle
17	chr2:172816800-172844200	Weak transcription	NHLF	lung
18	chr2:172817800-172845200	Weak transcription	Psoas Muscle	Psoas
19	chr2:172821000-172862800	Weak transcription	Brain Angular Gyrus	brain
20	chr2:172823000-172850400	Weak transcription	Right Ventricle	heart
21	chr2:172823200-172843600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:172823800-172842600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:172823800-172843800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:172823800-172844000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:172823800-172851200	Weak transcription	Fetal Kidney	kidney
26	chr2:172824000-172841000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:172824000-172841200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:172824000-172842600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:172824000-172857800	Weak transcription	Brain Anterior Caudate	brain
30	chr2:172824000-172857800	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:172824200-172850000	Weak transcription	NHDF-Ad	bronchial
32	chr2:172824200-172850400	Weak transcription	HMEC	breast
33	chr2:172824400-172843800	Weak transcription	NHEK	skin
34	chr2:172824400-172847200	Weak transcription	NH-A	brain
35	chr2:172825600-172842600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:172825800-172846400	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:172826200-172843200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:172826400-172848400	Weak transcription	Hela-S3	cervix
39	chr2:172828800-172841400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:172829200-172847000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:172829600-172841200	Weak transcription	HepG2	liver
42	chr2:172829600-172842000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:172829800-172848000	Weak transcription	HUVEC	blood vessel
44	chr2:172830600-172842400	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:172834400-172841000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:172834400-172842600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:172834400-172843200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:172834400-172843800	Weak transcription	Left Ventricle	heart
49	chr2:172834600-172843200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:172834600-172843400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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