Variant report

Variant	rs9373589
Chromosome Location	chr6:149707288-149707289
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	chr6:149706464..149708710-chr6:149709911..149712355,2	MCF-7	breast:
2	chr6:149703892..149707802-chr6:149748749..149751962,4	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11155640	0.87[LWK][hapmap];0.81[YRI][hapmap]
rs11155642	0.87[LWK][hapmap];0.81[YRI][hapmap]
rs11155645	0.81[YRI][hapmap]
rs11155647	0.81[YRI][hapmap]
rs12204461	0.81[YRI][hapmap]
rs12204793	0.81[YRI][hapmap]
rs12211357	0.81[YRI][hapmap]
rs17506789	0.85[YRI][hapmap]
rs1980774	0.80[YRI][hapmap]
rs2143076	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2262617	0.80[EUR][1000 genomes]
rs2341783	0.87[JPT][hapmap]
rs2341784	0.87[JPT][hapmap]
rs2744427	0.87[JPT][hapmap]
rs2744434	0.87[JPT][hapmap]
rs2789488	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2789490	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2789492	0.83[ASN][1000 genomes]
rs2789500	0.87[JPT][hapmap]
rs3734296	0.87[JPT][hapmap]
rs472810	0.85[JPT][hapmap]
rs474369	0.87[JPT][hapmap]
rs478767	0.87[JPT][hapmap]
rs480526	0.86[JPT][hapmap]
rs489551	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4895788	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4895789	0.95[CEU][hapmap]
rs4897124	0.80[EUR][1000 genomes]
rs492956	0.85[JPT][hapmap]
rs494340	0.82[JPT][hapmap]
rs501926	0.87[JPT][hapmap]
rs504762	0.82[JPT][hapmap]
rs504985	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs506268	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511100	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs511105	0.87[JPT][hapmap]
rs514839	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs515133	0.83[JPT][hapmap]
rs521845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532250	0.83[JPT][hapmap]
rs536203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs537354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538386	0.87[JPT][hapmap]
rs540538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs544947	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556335	0.87[JPT][hapmap]
rs559052	0.86[JPT][hapmap]
rs560051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs562428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs564961	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs565825	0.86[JPT][hapmap]
rs570442	0.82[JPT][hapmap]
rs577001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs579789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs580011	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs585022	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs600739	0.81[JPT][hapmap]
rs628488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs652807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs652921	0.87[JPT][hapmap]
rs6570965	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs663625	0.87[JPT][hapmap]
rs6911411	0.81[YRI][hapmap]
rs6932778	0.81[YRI][hapmap]
rs7349921	0.85[YRI][hapmap]
rs763590	0.81[YRI][hapmap]
rs7896	0.81[YRI][hapmap]
rs909793	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs9285519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9285520	0.86[LWK][hapmap];0.81[YRI][hapmap]
rs9322178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373592	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9377212	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9377218	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs9390676	0.86[JPT][hapmap]
rs9390677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9404034	0.87[JPT][hapmap]
rs9498322	0.81[YRI][hapmap]
rs9498323	0.83[YRI][hapmap]
rs9498324	0.87[LWK][hapmap];0.81[YRI][hapmap]
rs9498325	0.81[YRI][hapmap]
rs9498332	0.81[YRI][hapmap]
rs9498333	0.81[YRI][hapmap]
rs9498335	0.87[LWK][hapmap];0.81[YRI][hapmap]
rs9498336	0.81[YRI][hapmap]
rs9498337	0.81[YRI][hapmap]
rs9498338	0.81[YRI][hapmap]
rs9498341	0.81[YRI][hapmap]
rs9498342	0.80[YRI][hapmap]
rs997682	0.87[LWK][hapmap];0.81[YRI][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	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
rs9373589	RAET1E	cis	cerebellum	SCAN
rs9373589	LRP11	cis	parietal	SCAN
rs9373589	LRP11	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149682600-149709200	Weak transcription	Psoas Muscle	Psoas
2	chr6:149686000-149709000	Weak transcription	Stomach Mucosa	stomach
3	chr6:149687800-149726400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:149695400-149709600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:149697400-149708200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:149697600-149709000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:149697600-149713600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:149698400-149709600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:149698800-149707600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:149699000-149707800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:149700400-149709000	Weak transcription	Fetal Heart	heart
12	chr6:149700400-149728400	Weak transcription	Hela-S3	cervix
13	chr6:149700400-149732400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:149700600-149708000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:149700600-149709200	Weak transcription	Pancreas	Pancrea
16	chr6:149700600-149721200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:149700600-149721200	Weak transcription	Colonic Mucosa	Colon
18	chr6:149700600-149721200	Weak transcription	Right Ventricle	heart
19	chr6:149700600-149730800	Weak transcription	Fetal Brain Male	brain
20	chr6:149700800-149721000	Weak transcription	K562	blood
21	chr6:149700800-149721200	Weak transcription	Aorta	Aorta
22	chr6:149700800-149732800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:149701000-149710800	Weak transcription	NHDF-Ad	bronchial
24	chr6:149701200-149710200	Weak transcription	Esophagus	oesophagus
25	chr6:149701200-149721200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:149701400-149707600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:149701400-149707600	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:149701400-149709000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:149701400-149710800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:149701400-149717400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:149701400-149717800	Weak transcription	Fetal Kidney	kidney
32	chr6:149701400-149721200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:149701400-149730800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:149701400-149734200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:149701600-149707800	Weak transcription	Small Intestine	intestine
36	chr6:149701600-149712600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:149701600-149733600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:149702200-149709200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:149702400-149718800	Weak transcription	HUVEC	blood vessel
40	chr6:149702400-149721200	Weak transcription	Fetal Brain Female	brain
41	chr6:149702600-149707400	Weak transcription	A549	lung
42	chr6:149703000-149716000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:149703200-149708000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:149703200-149709200	Weak transcription	Gastric	stomach
45	chr6:149703200-149709200	Weak transcription	Ovary	ovary
46	chr6:149703200-149709400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:149703200-149717200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:149703200-149718400	Weak transcription	Thymus	Thymus
49	chr6:149703200-149719200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:149703200-149720400	Weak transcription	Brain Angular Gyrus	brain

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