Variant report

Variant	rs3782513
Chromosome Location	chr12:29506254-29506255
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:29506220-29506370	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:29505820..29507977-chr12:29508931..29512275,3	K562	blood:
2	chr12:29501467..29504234-chr12:29504488..29507414,2	K562	blood:
3	chr12:29504698..29507288-chr12:29512167..29514486,2	MCF-7	breast:
4	chr12:29501592..29504234-chr12:29504443..29507414,2	K562	blood:

Variant related genes	Relation type
ERGIC2	TF binding region
ENSG00000087502	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10082956	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10128781	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1035606	0.94[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1035607	0.99[EUR][1000 genomes]
rs10743657	0.83[AFR][1000 genomes]
rs10743658	0.83[AFR][1000 genomes]
rs10843377	0.81[LWK][hapmap]
rs10843390	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10843391	0.94[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10843397	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843398	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10843403	0.82[AFR][1000 genomes]
rs11050175	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11050203	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11050209	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1156242	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12320212	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12831751	0.94[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278093	0.94[ASW][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2278094	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3815843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931178	0.83[AFR][1000 genomes]
rs6487815	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7136223	0.82[AMR][1000 genomes]
rs7297435	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311742	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315504	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs7953619	0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9651802	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs966540	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs966541	0.81[AMR][1000 genomes]
rs996498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9989017	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][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	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1796867	chr12:29501941-29524159	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3782513	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs3782513	RP11-996F15.2	cis	Artery Tibial	GTEx
rs3782513	RP11-996F15.2	cis	Thyroid	GTEx
rs3782513	TMTC1	cis	parietal	SCAN
rs3782513	ERGIC2	cis	multi-tissue	Pritchard
rs3782513	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs3782513	ERGIC2	cis	lymphoblastoid	seeQTL
rs3782513	MLSTD1	cis	normal skin	skin_eQTL
rs3782513	RP11-996F15.2	cis	Stomach	GTEx
rs3782513	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs3782513	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs3782513	RP11-996F15.2	cis	lung	GTEx
rs3782513	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs3782513	IFLTD1	cis	parietal	SCAN
rs3782513	RP11-996F15.2	cis	Artery Aorta	GTEx
rs3782513	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
5	chr12:29473800-29522600	Weak transcription	NHEK	skin
6	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
7	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
9	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
15	chr12:29485600-29533400	Weak transcription	Gastric	stomach
16	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
17	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:29488800-29532000	Weak transcription	NHLF	lung
19	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:29489800-29510000	Weak transcription	Brain Germinal Matrix	brain
21	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
23	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:29491000-29511400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:29491400-29506400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:29492400-29511800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:29492400-29518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:29492800-29511800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:29492800-29519000	Weak transcription	HepG2	liver
30	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:29494400-29517800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
33	chr12:29494600-29509000	Weak transcription	Lung	lung
34	chr12:29494600-29511800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
36	chr12:29496400-29509200	Weak transcription	Left Ventricle	heart
37	chr12:29496400-29518000	Weak transcription	Brain Anterior Caudate	brain
38	chr12:29496400-29518000	Weak transcription	Thymus	Thymus
39	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:29496600-29517800	Weak transcription	NH-A	brain
41	chr12:29496800-29508600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:29496800-29519000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:29497000-29509000	Weak transcription	HMEC	breast
44	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
45	chr12:29497600-29518200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:29498000-29515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:29498800-29507800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:29498800-29509000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:29499000-29507600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr12:29499000-29532400	Weak transcription	Fetal Brain Female	brain

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