Variant report

Variant	rs4963859
Chromosome Location	chr12:25367838-25367839
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:25363402..25366108-chr12:25366322..25370146,4	K562	blood:
2	chr12:25367183..25369335-chr12:25401740..25404657,2	K562	blood:
3	chr12:25367414..25369461-chr12:25539857..25541737,2	K562	blood:
4	chr12:25353810..25355602-chr12:25365715..25367870,2	MCF-7	breast:
5	chr12:25365341..25368190-chr12:25372186..25374038,3	K562	blood:

Variant related genes	Relation type
ENSG00000133703	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10505959	0.90[JPT][hapmap]
rs10505960	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10505980	1.00[JPT][hapmap]
rs10771166	0.82[JPT][hapmap]
rs10771174	0.82[JPT][hapmap]
rs10771175	0.81[JPT][hapmap]
rs10842464	0.82[JPT][hapmap]
rs10842466	0.89[CHB][hapmap]
rs10842468	0.90[JPT][hapmap]
rs10842490	0.81[JPT][hapmap]
rs10842492	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10842494	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10842496	0.90[JPT][hapmap]
rs10842498	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10842499	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10842501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842502	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10842504	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842512	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10842514	1.00[JPT][hapmap]
rs11047824	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11047825	0.81[JPT][hapmap]
rs11047865	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs11047885	0.82[JPT][hapmap]
rs11047887	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047895	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047897	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047899	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047901	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047905	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047909	0.87[ASN][1000 genomes]
rs11047915	1.00[JPT][hapmap]
rs11047919	1.00[JPT][hapmap]
rs1137188	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1137189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1137196	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11608657	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11832421	0.89[CHB][hapmap]
rs11834088	0.82[JPT][hapmap]
rs12226937	0.91[JPT][hapmap]
rs12245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423443	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12424283	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578773	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579073	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579681	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580030	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581706	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12813551	1.00[JPT][hapmap]
rs12814233	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12815546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12820019	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12822857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1908946	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2291365	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs2352782	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4246228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4313666	0.82[JPT][hapmap]
rs4494384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4551857	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559767	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4963860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963861	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5009909	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61762422	0.92[AFR][1000 genomes]
rs6487461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487464	1.00[JPT][hapmap]
rs712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137630	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297103	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7298636	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs7299998	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7302922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303373	0.82[JPT][hapmap]
rs7306769	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7308865	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7312739	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7955844	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7960428	0.82[JPT][hapmap]
rs7976254	0.90[JPT][hapmap]
rs8720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634100	0.84[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1048631	chr12:25353517-25378661	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv898923	chr12:25357680-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv898924	chr12:25357680-25398972	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv557798	chr12:25359841-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv898925	chr12:25367669-25398972	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv898926	chr12:25367669-25408047	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4963859	LYRM5	cis	Thyroid	GTEx
rs4963859	LYRM5	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
3	chr12:25349000-25369200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:25349000-25372800	Weak transcription	Aorta	Aorta
5	chr12:25349000-25374200	Weak transcription	Lung	lung
6	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
7	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
8	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:25349400-25388600	Weak transcription	NHLF	lung
10	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
13	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
14	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
15	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:25349800-25379200	Weak transcription	Brain Anterior Caudate	brain
21	chr12:25349800-25386200	Weak transcription	Hela-S3	cervix
22	chr12:25349800-25390200	Weak transcription	K562	blood
23	chr12:25350000-25372600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:25350000-25402800	Weak transcription	Ovary	ovary
25	chr12:25353200-25378800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:25354400-25368200	Weak transcription	HUVEC	blood vessel
28	chr12:25354400-25369000	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:25354400-25378400	Weak transcription	HMEC	breast
30	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
31	chr12:25354600-25389000	Weak transcription	HSMMtube	muscle
32	chr12:25355400-25370600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr12:25355800-25396000	Weak transcription	Small Intestine	intestine
34	chr12:25356200-25372800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:25356600-25377600	Weak transcription	Gastric	stomach
36	chr12:25356600-25402600	Weak transcription	Fetal Heart	heart
37	chr12:25360200-25379200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:25360200-25380200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:25360400-25371200	Weak transcription	Fetal Lung	lung
40	chr12:25360400-25377000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:25360800-25388600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:25360800-25389200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:25360800-25402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:25361000-25376800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:25361000-25378600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:25361000-25379800	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:25361000-25383800	Weak transcription	NHEK	skin
48	chr12:25361000-25388000	Weak transcription	A549	lung
49	chr12:25361000-25388600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:25361000-25388800	Weak transcription	Esophagus	oesophagus

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