Variant report

Variant	rs9375543
Chromosome Location	chr6:128311140-128311141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128308101..128309848-chr6:128310756..128312690,2	MCF-7	breast:
2	chr6:128310427..128312557-chr6:128317983..128320683,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11154433	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12055782	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs13219424	0.81[ASN][1000 genomes]
rs1342646	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2024557	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2326670	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs3903662	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4113587	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4113588	0.92[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4563733	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6899650	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905941	0.80[MEX][hapmap]
rs6919966	0.82[CHD][hapmap]
rs6936878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs717851	0.84[CEU][hapmap];0.82[CHD][hapmap]
rs7742212	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7744108	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7758792	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9375542	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375544	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs9388610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9388612	1.00[ASN][1000 genomes]
rs9402011	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604642	chr6:128278798-128351143	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv7967	chr6:128304971-128315423	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
3	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9375543	HEY2	cis	cerebellum	SCAN
rs9375543	ENPP3	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128288600-128321800	Weak transcription	Small Intestine	intestine
2	chr6:128289000-128431000	Weak transcription	Psoas Muscle	Psoas
3	chr6:128293600-128374400	Weak transcription	Pancreas	Pancrea
4	chr6:128294400-128330600	Weak transcription	NHDF-Ad	bronchial
5	chr6:128297400-128334000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:128297800-128312600	Weak transcription	Colonic Mucosa	Colon
7	chr6:128298000-128352600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:128298200-128313800	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:128298200-128334600	Weak transcription	Fetal Heart	heart
10	chr6:128299000-128317200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:128300000-128317000	Weak transcription	Primary T cells from cord blood	blood
12	chr6:128300400-128312800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:128300800-128313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:128300800-128326400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:128301000-128325200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:128302600-128319600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:128302600-128331400	Weak transcription	Gastric	stomach
18	chr6:128302800-128313400	Weak transcription	Brain Angular Gyrus	brain
19	chr6:128302800-128321600	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:128302800-128325400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:128302800-128327800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:128302800-128343800	Weak transcription	Ovary	ovary
23	chr6:128303000-128312600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:128303000-128321800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:128303400-128313000	Weak transcription	Adipose Nuclei	Adipose
26	chr6:128303800-128320400	Weak transcription	Fetal Intestine Small	intestine
27	chr6:128304000-128329200	Weak transcription	Fetal Lung	lung
28	chr6:128304600-128327600	Weak transcription	Fetal Stomach	stomach
29	chr6:128304600-128328600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:128304800-128321600	Weak transcription	Brain Substantia Nigra	brain
31	chr6:128305200-128326200	Weak transcription	Osteobl	bone
32	chr6:128305200-128353000	Weak transcription	Left Ventricle	heart
33	chr6:128305800-128313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:128305800-128319000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:128306000-128329000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:128306000-128334000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:128306000-128343200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:128306200-128311200	Weak transcription	Fetal Thymus	thymus
39	chr6:128306400-128311200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:128306400-128314000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:128306800-128311200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:128306800-128327800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:128307000-128317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:128307000-128326200	Weak transcription	HMEC	breast
45	chr6:128307200-128327600	Weak transcription	Placenta	Placenta
46	chr6:128307200-128340800	Weak transcription	HSMMtube	muscle
47	chr6:128307400-128329000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:128307600-128311200	Weak transcription	Fetal Intestine Large	intestine
49	chr6:128307600-128313200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:128307600-128317400	Weak transcription	NHEK	skin

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