Variant report

Variant	rs9349685
Chromosome Location	chr6:53746756-53746757
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	chr6:53658255..53661038-chr6:53744505..53747227,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10755766	0.81[AMR][1000 genomes]
rs1076701	0.93[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1076702	0.93[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10948775	0.81[AMR][1000 genomes]
rs2073020	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2294789	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2294790	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2294791	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3777661	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4265034	0.83[ASN][1000 genomes]
rs4314499	0.84[AMR][1000 genomes]
rs4624872	0.81[ASN][1000 genomes]
rs6903399	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9296722	0.83[ASN][1000 genomes]
rs9357776	0.93[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9370233	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9370241	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9370244	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9382232	0.81[AMR][1000 genomes]
rs9382233	0.81[AMR][1000 genomes]
rs9382238	0.87[EUR][1000 genomes]
rs9382241	0.88[EUR][1000 genomes]
rs9382243	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382244	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382246	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9382248	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382252	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9382253	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382254	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382256	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9382257	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9395876	0.81[AMR][1000 genomes]
rs9395878	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9395881	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9395884	0.81[ASN][1000 genomes]
rs9395887	0.83[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
5	chr6:53729400-53748000	Weak transcription	HepG2	liver
6	chr6:53730200-53748200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
8	chr6:53732000-53747800	Weak transcription	HSMMtube	muscle
9	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
10	chr6:53735000-53751800	Weak transcription	Gastric	stomach
11	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
12	chr6:53736200-53751400	Weak transcription	Brain Substantia Nigra	brain
13	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
14	chr6:53738400-53747800	Weak transcription	Fetal Thymus	thymus
15	chr6:53739000-53753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:53739000-53753600	Weak transcription	NHEK	skin
17	chr6:53739000-53767800	Weak transcription	Ovary	ovary
18	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
19	chr6:53740000-53750600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:53740000-53752400	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:53740000-53755200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:53740200-53747800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:53740400-53754000	Weak transcription	HSMM	muscle
24	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:53742200-53748000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
28	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
29	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:53742600-53748000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
33	chr6:53744200-53752200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:53744400-53748200	Weak transcription	Dnd41	blood
35	chr6:53744600-53764200	Weak transcription	Fetal Intestine Small	intestine
36	chr6:53744800-53752200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:53744800-53760400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:53745400-53760600	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:53745600-53762200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:53746200-53757200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:53746200-53758000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:53746400-53758600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:53746400-53762000	Weak transcription	Rectal Mucosa Donor 31	rectum

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