Variant report

Variant	rs2682427
Chromosome Location	chr12:123656809-123656810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123656463..123658655-chr12:123663135..123665180,2	K562	blood:
2	chr12:123656463..123658655-chr12:123663135..123666317,3	K562	blood:

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10444439	0.81[JPT][hapmap]
rs1051434	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10773000	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10773003	0.85[JPT][hapmap]
rs10773005	0.85[JPT][hapmap]
rs10846489	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10848428	0.85[JPT][hapmap]
rs11057189	0.80[ASN][1000 genomes]
rs11057223	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11057251	0.85[JPT][hapmap]
rs11057276	0.85[JPT][hapmap]
rs1109559	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1109560	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs11608305	0.85[JPT][hapmap]
rs11610710	0.95[ASN][1000 genomes]
rs12229700	0.95[ASN][1000 genomes]
rs12317452	0.85[JPT][hapmap]
rs12366872	0.85[JPT][hapmap]
rs1568428	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1611973	0.85[ASN][1000 genomes]
rs1615350	0.84[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1616484	0.81[ASN][1000 genomes]
rs1626703	0.87[ASN][1000 genomes]
rs1716178	0.89[ASN][1000 genomes]
rs1716184	0.88[ASN][1000 genomes]
rs1727286	0.95[ASN][1000 genomes]
rs1727293	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1727295	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1727301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727302	0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1727305	0.87[ASN][1000 genomes]
rs1727307	0.85[JPT][hapmap]
rs1727312	0.87[ASN][1000 genomes]
rs1790088	0.95[ASN][1000 genomes]
rs1790094	0.85[JPT][hapmap]
rs1790096	0.88[ASN][1000 genomes]
rs1790104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1790106	0.85[JPT][hapmap]
rs1790121	0.85[JPT][hapmap]
rs1790129	0.93[ASN][1000 genomes]
rs1790134	0.93[ASN][1000 genomes]
rs1879379	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2102949	0.82[ASN][1000 genomes]
rs2271976	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2337630	0.80[ASN][1000 genomes]
rs2337631	0.80[ASN][1000 genomes]
rs3088303	0.85[JPT][hapmap]
rs3759111	0.92[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs3759113	0.92[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4148863	0.85[JPT][hapmap]
rs4460848	0.92[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4759367	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4759377	0.85[JPT][hapmap]
rs4759406	0.82[ASN][1000 genomes]
rs4759407	0.92[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs60296110	0.82[ASN][1000 genomes]
rs7139321	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7315453	0.85[JPT][hapmap]
rs73231928	0.82[ASN][1000 genomes]
rs7972811	0.85[JPT][hapmap]
rs949143	0.85[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	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
2	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2682427	MGC7036	Cis_1M	lymphoblastoid	RTeQTL
rs2682427	DDX55	cis	parietal	SCAN
rs2682427	RILPL2	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123660800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:123636600-123676200	Weak transcription	Gastric	stomach
3	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
4	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
5	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
6	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
7	chr12:123637000-123673400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
12	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:123640600-123657800	Weak transcription	NHLF	lung
14	chr12:123645400-123660000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:123645600-123660800	Weak transcription	Fetal Brain Male	brain
16	chr12:123647400-123660800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:123648400-123679200	Strong transcription	Thymus	Thymus
18	chr12:123648800-123673600	Weak transcription	HMEC	breast
19	chr12:123649000-123658400	Weak transcription	HUVEC	blood vessel
20	chr12:123649200-123660800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:123650000-123660600	Weak transcription	Fetal Kidney	kidney
22	chr12:123650400-123686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:123650600-123658000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:123650600-123658000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:123650600-123660800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:123650600-123660800	Weak transcription	HSMM	muscle
27	chr12:123650600-123664600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:123650600-123664600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:123650600-123671600	Weak transcription	Brain Germinal Matrix	brain
30	chr12:123650600-123673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:123650600-123685800	Weak transcription	Small Intestine	intestine
32	chr12:123650600-123687200	Weak transcription	Pancreas	Pancrea
33	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:123650800-123657800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:123650800-123657800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:123650800-123663600	Weak transcription	Lung	lung
37	chr12:123651000-123658000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:123651200-123659400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:123651200-123660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:123651200-123661200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:123651200-123670000	Weak transcription	Spleen	Spleen
42	chr12:123651200-123673600	Weak transcription	Brain Substantia Nigra	brain
43	chr12:123651400-123657800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:123651400-123658000	Weak transcription	Adipose Nuclei	Adipose
45	chr12:123651400-123660800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:123651400-123660800	Weak transcription	Osteobl	bone
47	chr12:123651400-123662600	Weak transcription	Brain Anterior Caudate	brain
48	chr12:123651400-123663200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:123651400-123672000	Weak transcription	NHDF-Ad	bronchial
50	chr12:123651400-123673600	Weak transcription	Rectal Mucosa Donor 31	rectum

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