Variant report

Variant	rs2744432
Chromosome Location	chr6:149743871-149743872
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149742080..149743974-chr6:149748766..149751309,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs17086451	0.87[ASN][1000 genomes]
rs2143076	0.91[JPT][hapmap];0.80[AMR][1000 genomes]
rs2341783	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2341784	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2744427	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2744431	0.82[ASN][1000 genomes]
rs2744433	0.87[ASN][1000 genomes]
rs2744434	0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2789487	0.83[ASN][1000 genomes]
rs2789488	0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs2789489	0.83[ASN][1000 genomes]
rs2789490	0.86[JPT][hapmap]
rs2789492	0.80[AMR][1000 genomes]
rs2789500	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs3734296	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs4360154	0.83[ASN][1000 genomes]
rs472810	0.95[JPT][hapmap]
rs474369	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs478767	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs480526	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs480778	0.85[ASN][1000 genomes]
rs4895788	0.87[AMR][1000 genomes]
rs4897117	0.85[ASN][1000 genomes]
rs492956	0.95[JPT][hapmap]
rs494340	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs501926	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs504762	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs504985	0.82[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs506268	0.86[JPT][hapmap]
rs511105	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs513923	0.87[ASN][1000 genomes]
rs514839	0.82[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs515133	0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs521845	0.82[CEU][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs527971	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs532250	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs536203	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs537354	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs538386	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs540538	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs556335	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs559052	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs560051	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs562428	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs565825	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs570442	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs577001	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs579789	0.91[JPT][hapmap]
rs585022	0.82[AMR][1000 genomes]
rs588028	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs60006373	0.87[ASN][1000 genomes]
rs600739	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs630642	0.82[ASN][1000 genomes]
rs638407	0.82[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes]
rs641068	0.87[ASN][1000 genomes]
rs652514	0.88[ASN][1000 genomes]
rs652807	0.82[CEU][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes]
rs652921	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6570965	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs663625	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs909793	0.82[JPT][hapmap]
rs9285519	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs9322178	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs9373589	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs9373592	0.84[AMR][1000 genomes]
rs9377216	0.87[ASN][1000 genomes]
rs9377217	0.83[ASN][1000 genomes]
rs9377218	0.86[JPT][hapmap]
rs9390676	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs9390677	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs9399686	0.83[ASN][1000 genomes]
rs9404034	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs9404037	0.82[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	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2744432	LRP11	cis	parietal	SCAN
rs2744432	LRP11	cis	cerebellum	SCAN
rs2744432	RAET1E	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149709600-149750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:149721800-149744800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:149721800-149745200	Weak transcription	Pancreas	Pancrea
4	chr6:149722000-149745000	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:149725200-149744600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:149728200-149744600	Weak transcription	Fetal Intestine Small	intestine
7	chr6:149730600-149744400	Weak transcription	NHDF-Ad	bronchial
8	chr6:149731600-149744200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:149731600-149744400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:149731600-149744600	Weak transcription	NHLF	lung
11	chr6:149731600-149745200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:149731600-149745200	Weak transcription	Left Ventricle	heart
13	chr6:149731600-149745200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:149731800-149744400	Weak transcription	Brain Substantia Nigra	brain
15	chr6:149731800-149744400	Weak transcription	HSMMtube	muscle
16	chr6:149731800-149745200	Weak transcription	Fetal Brain Female	brain
17	chr6:149732000-149744400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:149732000-149744600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:149732200-149744400	Weak transcription	Ovary	ovary
20	chr6:149732200-149744400	Weak transcription	Osteobl	bone
21	chr6:149732200-149745000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:149732400-149744000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:149732400-149744400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:149732400-149744400	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:149732400-149745200	Weak transcription	Brain Germinal Matrix	brain
26	chr6:149732600-149744600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:149732600-149744600	Weak transcription	Fetal Lung	lung
28	chr6:149732600-149744800	Weak transcription	NH-A	brain
29	chr6:149732600-149745400	Weak transcription	Dnd41	blood
30	chr6:149732800-149744600	Weak transcription	HSMM	muscle
31	chr6:149732800-149744800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:149733200-149744800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:149733400-149744600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:149733400-149744800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:149733600-149744800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:149735000-149744400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:149735400-149744400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:149735600-149744200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:149735600-149744400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:149735600-149744800	Weak transcription	Adipose Nuclei	Adipose
41	chr6:149736200-149744200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:149739800-149744800	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:149742000-149745000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:149743800-149744000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:149743800-149744400	Enhancers	Placenta	Placenta
46	chr6:149743800-149744400	Enhancers	Lung	lung

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