Variant report

Variant	rs12692437
Chromosome Location	chr2:11480561-11480562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11479515..11481764-chr2:11513114..11514767,2	MCF-7	breast:
2	chr2:11479664..11482372-chr6:149351829..149354615,2	MCF-7	breast:
3	chr2:11465940..11468205-chr2:11479384..11482432,3	MCF-7	breast:
4	chr2:11479749..11482125-chr2:11482379..11485689,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10173492	0.84[AMR][1000 genomes]
rs10178332	0.93[CEU][hapmap]
rs10192593	0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap]
rs10192994	0.93[CEU][hapmap]
rs10194620	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs10203916	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap]
rs10205944	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap]
rs10210600	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs10454126	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs10929732	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs11694729	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs11695377	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs12467103	0.84[AMR][1000 genomes]
rs12692434	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs12692435	0.86[YRI][hapmap]
rs12990641	0.86[CEU][hapmap]
rs12992581	0.86[YRI][hapmap]
rs13015560	0.86[CEU][hapmap]
rs13016386	0.81[AMR][1000 genomes]
rs13017021	0.86[CEU][hapmap]
rs1562748	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs1562749	0.93[CEU][hapmap]
rs1868584	0.93[CEU][hapmap]
rs1901011	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2044758	0.93[CEU][hapmap]
rs2060635	0.80[AMR][1000 genomes]
rs2084577	1.00[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2122384	0.82[YRI][hapmap]
rs2357996	0.93[CEU][hapmap]
rs3911110	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs4303693	0.93[CEU][hapmap]
rs4668720	0.83[YRI][hapmap]
rs4668721	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4669709	0.84[AMR][1000 genomes]
rs4669710	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs4669711	0.84[AMR][1000 genomes]
rs4669712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669713	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669715	0.93[CEU][hapmap]
rs62118012	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6432183	0.93[CEU][hapmap]
rs6432184	0.93[CEU][hapmap]
rs6432186	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs6706126	0.84[AMR][1000 genomes]
rs6710031	0.93[CEU][hapmap]
rs6713273	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs6721445	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs6730673	0.87[GIH][hapmap];0.83[YRI][hapmap]
rs6733312	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs6735090	0.84[AMR][1000 genomes]
rs6736240	0.82[YRI][hapmap]
rs6749456	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs6755196	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs6755337	0.87[GIH][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap]
rs6759490	0.87[GIH][hapmap];0.92[MEX][hapmap]
rs6760802	0.93[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs7355446	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7355489	0.87[GIH][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap]
rs753770	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap]
rs7558664	0.87[GIH][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap]
rs7563468	0.87[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs7563928	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7568064	0.83[YRI][hapmap]
rs7575837	0.86[YRI][hapmap]
rs7593091	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs9287728	0.93[CEU][hapmap]
rs965665	0.93[CEU][hapmap]

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	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12692437	IAH1	cis	cerebellum	SCAN
rs12692437	ROCK2	cis	cerebellum	SCAN
rs12692437	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:11467600-11481600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:11468400-11481200	Weak transcription	HUVEC	blood vessel
4	chr2:11470400-11481400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:11470800-11481200	Weak transcription	Right Atrium	heart
6	chr2:11470800-11481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:11471000-11481200	Weak transcription	HSMM	muscle
8	chr2:11472200-11482800	Weak transcription	Gastric	stomach
9	chr2:11475000-11481200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:11475400-11481000	Weak transcription	Ovary	ovary
11	chr2:11475800-11481200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:11476200-11482200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:11476600-11482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:11476600-11482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:11476800-11481000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:11476800-11481000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:11476800-11481200	Weak transcription	Psoas Muscle	Psoas
18	chr2:11476800-11482200	Weak transcription	Left Ventricle	heart
19	chr2:11476800-11482600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:11477200-11482200	Weak transcription	Fetal Stomach	stomach
21	chr2:11477800-11481000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:11478800-11480800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:11478800-11481000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:11478800-11481200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:11479000-11480600	Flanking Active TSS	HepG2	liver
26	chr2:11479000-11481000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:11479000-11482600	Weak transcription	Right Ventricle	heart
28	chr2:11479600-11480800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:11479600-11482000	Enhancers	Colon Smooth Muscle	Colon
30	chr2:11479800-11480600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:11479800-11480600	Enhancers	Small Intestine	intestine
32	chr2:11479800-11480600	Flanking Active TSS	A549	lung
33	chr2:11479800-11480800	Weak transcription	Fetal Kidney	kidney
34	chr2:11479800-11481000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:11479800-11481000	Enhancers	Liver	Liver
36	chr2:11479800-11481000	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr2:11479800-11481000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:11479800-11481000	Enhancers	HMEC	breast
39	chr2:11479800-11481200	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:11479800-11481200	Enhancers	Dnd41	blood
41	chr2:11479800-11481400	Enhancers	Stomach Mucosa	stomach
42	chr2:11479800-11481800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:11479800-11482200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:11479800-11482200	Enhancers	Fetal Lung	lung
45	chr2:11479800-11485400	Active TSS	GM12878-XiMat	blood
46	chr2:11480000-11480600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:11480000-11480800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:11480000-11481000	Enhancers	Adipose Nuclei	Adipose
49	chr2:11480000-11481200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:11480000-11481200	Enhancers	NHDF-Ad	bronchial

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