Variant report

Variant	rs12472676
Chromosome Location	chr2:86510815-86510816
allele	C/T
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	ESR1	chr2:86510459-86510880	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr2:86510509-86510902	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr2:86510782-86510831	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:86510767-86510845	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:86510691-86510852	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86506964..86508906-chr2:86509472..86512092,2	K562	blood:

Variant related genes	Relation type
REEP1	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10186289	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs10189492	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10200186	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200619	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10201457	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10520415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11127026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127028	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11127029	0.85[CEU][hapmap]
rs11674249	0.81[ASN][1000 genomes]
rs11675942	0.82[JPT][hapmap]
rs11681689	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs11685863	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11691726	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs11691807	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12052607	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs12466728	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs12469233	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12472390	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476706	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12476826	0.83[JPT][hapmap]
rs12478575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478653	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620833	1.00[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12622200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12714179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988844	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12999029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13015186	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13017143	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13017338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13018801	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13020869	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023154	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13024964	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13421310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17438687	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs17737955	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17738096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863051	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1863052	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1863059	0.82[JPT][hapmap]
rs1863063	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs2278105	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2367233	0.85[CEU][hapmap]
rs34048420	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34069316	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160687	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35281683	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35370705	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35494267	0.80[ASN][1000 genomes]
rs35762338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392258	0.99[ASN][1000 genomes]
rs4832031	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832033	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4832261	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832262	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4832269	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4832270	0.82[JPT][hapmap]
rs6547668	0.83[JPT][hapmap]
rs6547673	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6547674	0.84[CEU][hapmap]
rs6713456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714362	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6725234	0.89[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6738585	0.80[ASN][1000 genomes]
rs67407963	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6745235	0.83[JPT][hapmap]
rs6746198	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs67903513	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560886	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7563887	0.85[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7571424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7593440	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9677502	0.82[CEU][hapmap];0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12472676	IMMT	cis	Whole Blood	GTEx
rs12472676	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs12472676	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs12472676	MRPL35	cis	uninvolved skin	skin_eQTL

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86500000-86517400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:86502800-86513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:86506200-86512400	Enhancers	Left Ventricle	heart
4	chr2:86506600-86511800	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr2:86506800-86513200	Enhancers	Colon Smooth Muscle	Colon
6	chr2:86507600-86511000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:86508000-86511000	Weak transcription	Brain Anterior Caudate	brain
8	chr2:86508000-86520200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:86508200-86519800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:86508400-86511200	Weak transcription	HSMMtube	muscle
11	chr2:86508400-86513000	Bivalent Enhancer	Fetal Stomach	stomach
12	chr2:86508400-86517600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:86508600-86518400	Weak transcription	Fetal Brain Male	brain
14	chr2:86509000-86511600	Weak transcription	Fetal Brain Female	brain
15	chr2:86509600-86511000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:86509600-86511200	Enhancers	Aorta	Aorta
17	chr2:86509600-86512400	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:86509600-86514000	Enhancers	Right Ventricle	heart
19	chr2:86509800-86511600	Enhancers	Fetal Heart	heart
20	chr2:86509800-86511800	Enhancers	Fetal Intestine Large	intestine
21	chr2:86510000-86512000	Enhancers	Placenta	Placenta
22	chr2:86510000-86512200	Enhancers	Psoas Muscle	Psoas
23	chr2:86510200-86511000	Enhancers	Fetal Kidney	kidney
24	chr2:86510200-86511200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:86510200-86512400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:86510400-86511200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:86510400-86511200	Enhancers	Stomach Mucosa	stomach
28	chr2:86510400-86511800	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:86510400-86512200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:86510400-86512200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr2:86510400-86513000	Enhancers	Fetal Lung	lung
32	chr2:86510400-86513400	Enhancers	Fetal Muscle Trunk	muscle
33	chr2:86510400-86514400	Enhancers	Fetal Muscle Leg	muscle
34	chr2:86510600-86511000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:86510600-86511000	Weak transcription	Lung	lung
36	chr2:86510600-86511200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr2:86510600-86512200	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr2:86510600-86512600	Enhancers	Right Atrium	heart
39	chr2:86510600-86514000	Enhancers	Pancreas	Pancrea
40	chr2:86510800-86511200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:86510800-86511200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:86510800-86511200	Enhancers	Esophagus	oesophagus
43	chr2:86510800-86511400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:86510800-86511400	Enhancers	Colonic Mucosa	Colon
45	chr2:86510800-86511600	Weak transcription	Brain Germinal Matrix	brain
46	chr2:86510800-86511600	Bivalent Enhancer	HepG2	liver
47	chr2:86510800-86511800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:86510800-86512000	Genic enhancers	Fetal Intestine Small	intestine
49	chr2:86510800-86512000	Enhancers	Gastric	stomach
50	chr2:86510800-86512200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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