Variant report

Variant	rs9402035
Chromosome Location	chr6:128661301-128661302
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	chr6:128660307..128662449-chr6:128682596..128686708,3	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10428737	1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap]
rs11753971	1.00[CHD][hapmap]
rs11964875	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs11965122	0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs11965141	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs11966128	0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs1339189	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1339196	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs1416517	0.92[CEU][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1538498	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1612415	0.91[CEU][hapmap]
rs17055564	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17055574	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17055596	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17055597	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs17055601	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17055604	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs17055608	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs17055611	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17055612	0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17055616	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs17055617	1.00[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17055618	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs17055619	0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17055628	0.90[EUR][1000 genomes]
rs17055630	0.94[EUR][1000 genomes]
rs17055679	0.94[EUR][1000 genomes]
rs17055689	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs17055706	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs17055717	0.92[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs17055719	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17055727	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs17055733	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs17055854	1.00[CHD][hapmap];0.85[MEX][hapmap];0.93[YRI][hapmap]
rs17343887	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17353545	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs17430131	0.92[CEU][hapmap]
rs17430452	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17456343	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17456385	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17456601	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1768353	1.00[CHD][hapmap]
rs1768357	1.00[CHD][hapmap]
rs1768360	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap]
rs1891146	0.93[YRI][hapmap]
rs1891147	0.92[YRI][hapmap]
rs2027311	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4267969	0.94[EUR][1000 genomes]
rs4466261	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs55969073	0.94[EUR][1000 genomes]
rs56095177	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56241890	0.94[EUR][1000 genomes]
rs57318936	0.94[EUR][1000 genomes]
rs59132771	0.94[EUR][1000 genomes]
rs6420738	0.85[EUR][1000 genomes]
rs6913718	0.92[EUR][1000 genomes]
rs6931769	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs6933821	0.92[CEU][hapmap]
rs6939023	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs722796	0.93[YRI][hapmap]
rs72967026	0.94[EUR][1000 genomes]
rs72967039	0.94[EUR][1000 genomes]
rs72967046	0.94[EUR][1000 genomes]
rs72967053	0.92[EUR][1000 genomes]
rs72967056	0.92[EUR][1000 genomes]
rs72967058	0.94[EUR][1000 genomes]
rs72967074	0.94[EUR][1000 genomes]
rs72967078	0.92[EUR][1000 genomes]
rs72967081	0.92[EUR][1000 genomes]
rs72967087	0.92[EUR][1000 genomes]
rs72967090	0.92[EUR][1000 genomes]
rs72969051	0.85[EUR][1000 genomes]
rs72969054	0.94[EUR][1000 genomes]
rs72969059	0.94[EUR][1000 genomes]
rs72969061	0.94[EUR][1000 genomes]
rs72969063	0.94[EUR][1000 genomes]
rs72969067	0.94[EUR][1000 genomes]
rs72969070	0.94[EUR][1000 genomes]
rs72969074	0.94[EUR][1000 genomes]
rs72969075	0.92[EUR][1000 genomes]
rs72969078	0.92[EUR][1000 genomes]
rs72969081	0.86[EUR][1000 genomes]
rs72969088	0.85[EUR][1000 genomes]
rs72969090	0.85[EUR][1000 genomes]
rs72969093	0.85[EUR][1000 genomes]
rs72969097	0.94[EUR][1000 genomes]
rs72969098	0.92[EUR][1000 genomes]
rs72971103	0.94[EUR][1000 genomes]
rs72971104	0.85[EUR][1000 genomes]
rs72972078	0.85[EUR][1000 genomes]
rs72972082	0.94[EUR][1000 genomes]
rs72972084	0.94[EUR][1000 genomes]
rs72972086	0.94[EUR][1000 genomes]
rs72972090	0.83[EUR][1000 genomes]
rs72972091	0.85[EUR][1000 genomes]
rs72974006	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72974007	1.00[ASN][1000 genomes]
rs72974013	1.00[ASN][1000 genomes]
rs7764930	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs7771630	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs7773248	0.92[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs7776405	0.94[EUR][1000 genomes]
rs9321114	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs9372888	0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs9375562	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946424	0.93[YRI][hapmap]
rs9491939	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs953549	0.85[CEU][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128632200-128665200	Weak transcription	Gastric	stomach
2	chr6:128635600-128672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:128641400-128661400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:128649200-128661400	Weak transcription	Pancreas	Pancrea
5	chr6:128649200-128665600	Weak transcription	Left Ventricle	heart
6	chr6:128649400-128671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:128649400-128678600	Weak transcription	HSMM	muscle
8	chr6:128649600-128661600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:128656400-128661400	Enhancers	Colon Smooth Muscle	Colon
10	chr6:128657800-128667800	Weak transcription	Fetal Kidney	kidney
11	chr6:128658800-128661400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:128659800-128661600	Enhancers	Fetal Intestine Small	intestine
13	chr6:128659800-128671400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:128660000-128666200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:128660000-128667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:128660000-128667800	Weak transcription	Ovary	ovary
17	chr6:128660400-128661400	Enhancers	Brain Cingulate Gyrus	brain
18	chr6:128660400-128661600	Enhancers	Fetal Intestine Large	intestine
19	chr6:128660600-128661400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:128660600-128661400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:128660600-128661400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:128660600-128661400	Enhancers	Rectal Smooth Muscle	rectum
23	chr6:128660600-128661600	Flanking Active TSS	Liver	Liver
24	chr6:128660600-128661800	Enhancers	Fetal Brain Male	brain
25	chr6:128660600-128661800	Enhancers	Fetal Heart	heart
26	chr6:128660600-128661800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr6:128660600-128662800	Enhancers	Fetal Lung	lung
28	chr6:128660800-128661600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:128660800-128661600	Enhancers	Adipose Nuclei	Adipose
30	chr6:128660800-128661600	Enhancers	Psoas Muscle	Psoas
31	chr6:128660800-128661600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:128660800-128661600	Enhancers	Small Intestine	intestine
33	chr6:128660800-128661600	Flanking Active TSS	HepG2	liver
34	chr6:128660800-128661600	Enhancers	HSMMtube	muscle
35	chr6:128660800-128661800	Enhancers	Stomach Mucosa	stomach
36	chr6:128660800-128661800	Enhancers	NHDF-Ad	bronchial
37	chr6:128661000-128661400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr6:128661000-128661600	Enhancers	Brain Hippocampus Middle	brain
39	chr6:128661000-128661600	Enhancers	Brain Substantia Nigra	brain
40	chr6:128661000-128661600	Enhancers	A549	lung
41	chr6:128661000-128661600	Enhancers	Osteobl	bone
42	chr6:128661200-128661400	Enhancers	NHLF	lung
43	chr6:128661200-128661600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:128661200-128661600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:128661200-128661800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:128661200-128661800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr6:128661200-128664400	Weak transcription	Fetal Stomach	stomach
48	chr6:128661200-128665200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:128661200-128667800	Weak transcription	Brain Anterior Caudate	brain

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