Variant report

Variant	rs12093623
Chromosome Location	chr1:76256232-76256233
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	POLR2A	chr1:76256156-76256996	K562	blood:	n/a	n/a
3	POLR2A	chr1:76255728-76256819	K562	blood:	n/a	n/a
4	POLR2A	chr1:76256191-76256857	K562	blood:	n/a	n/a
5	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
6	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
8	POLR2A	chr1:76251073-76257428	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:76251198-76257365	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:76251042-76257307	U87	brain:	n/a	n/a
11	POLR2A	chr1:76256215-76256363	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:76251108-76257452	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:76255480-76256281	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr1:76256200-76256663	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:76256223-76256972	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:76256226-76257332	K562	blood:	n/a	n/a
18	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:76256198-76256790	HCT-116	colon:	n/a	n/a
21	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
22	POLR2A	chr1:76250200-76257400	GM19099	blood:	n/a	n/a
23	POLR2A	chr1:76255628-76257400	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:76255510-76257063	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr1:76250996-76257615	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:76251203-76256991	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr1:76256223-76256527	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:76250185-76257476	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:76251241-76256430	U87	brain:	n/a	n/a
30	POLR2A	chr1:76255688-76257449	HUVEC	blood vessel:	n/a	n/a
31	CHD1	chr1:76256206-76256264	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:76251219-76256431	U87	brain:	n/a	n/a
33	POLR2A	chr1:76250012-76264059	K562	blood:	n/a	n/a
34	POLR2A	chr1:76256064-76257003	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:76255753-76256558	HCT-116	colon:	n/a	n/a
36	POLR2A	chr1:76254458-76256363	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:76251020-76258361	U87	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
2	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
3	chr1:76213598..76215985-chr1:76254500..76257122,2	K562	blood:

No data

Variant related genes	Relation type
RABGGTB	TF binding region
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1061337	0.80[AMR][1000 genomes]
rs10732723	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs10782558	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11161510	0.80[AMR][1000 genomes]
rs11161515	0.80[AMR][1000 genomes]
rs11161521	0.80[AMR][1000 genomes]
rs11161620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161626	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161792	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11161836	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs11161857	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs1144336	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146646	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146653	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588578	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs1159214	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs12021855	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12090849	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12094842	0.84[EUR][1000 genomes]
rs12122939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127078	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136360	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12723575	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1565717	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1770885	0.81[CEU][hapmap]
rs1770887	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2029681	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2029683	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs2172507	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2172508	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2347962	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28602663	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2881786	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4949677	0.91[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4949885	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267813	0.82[EUR][1000 genomes]
rs56352044	0.80[EUR][1000 genomes]
rs5745336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745390	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745427	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745433	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745442	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs5745449	1.00[CHB][hapmap]
rs61289992	0.80[AMR][1000 genomes]
rs61770533	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799967	0.80[AMR][1000 genomes]
rs61799990	0.85[EUR][1000 genomes]
rs6678348	0.85[EUR][1000 genomes]
rs6683437	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs6699682	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs72686191	0.80[AMR][1000 genomes]
rs7516226	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7523573	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7538800	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7547056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549863	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs931507	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs9662166	0.84[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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12093623	ACADM	cis	Whole Blood	GTEx
rs12093623	MSH4	cis	Artery Tibial	GTEx
rs12093623	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76252200-76258400	Weak transcription	Spleen	Spleen
2	chr1:76252400-76258800	Transcr. at gene 5' and 3'	K562	blood
3	chr1:76252600-76257600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:76252800-76256800	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr1:76252800-76257000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
6	chr1:76252800-76257000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:76252800-76257200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
8	chr1:76253000-76256800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
9	chr1:76253000-76257400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
10	chr1:76253200-76256600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:76253200-76256600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:76253200-76257400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:76253400-76256800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:76253600-76256800	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:76253600-76257400	Transcr. at gene 5' and 3'	Hela-S3	cervix
16	chr1:76253800-76257000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr1:76254000-76256600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:76254000-76257000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:76254000-76260000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:76254200-76257400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:76254200-76258400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:76254200-76258600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
23	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:76254400-76256400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:76254400-76256400	Weak transcription	Pancreas	Pancrea
26	chr1:76254400-76256600	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr1:76254400-76256600	Genic enhancers	Adipose Nuclei	Adipose
28	chr1:76254400-76256800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
29	chr1:76254400-76257400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:76254400-76262400	Strong transcription	Placenta	Placenta
31	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:76254600-76256800	Transcr. at gene 5' and 3'	NHEK	skin
33	chr1:76254600-76257000	Transcr. at gene 5' and 3'	A549	lung
34	chr1:76254600-76257600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr1:76254800-76256600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:76254800-76256800	Genic enhancers	Fetal Intestine Large	intestine
37	chr1:76254800-76258200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr1:76254800-76258400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr1:76254800-76262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:76254800-76262600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:76255000-76256400	Weak transcription	Aorta	Aorta
42	chr1:76255000-76256400	Genic enhancers	Liver	Liver
43	chr1:76255000-76256800	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr1:76255000-76257000	Transcr. at gene 5' and 3'	HepG2	liver
45	chr1:76255000-76257200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
46	chr1:76255000-76257400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:76255200-76256400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:76255200-76256400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:76255200-76256400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr1:76255200-76256400	Enhancers	Skeletal Muscle Male	skeletal muscle

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