Variant report

Variant	rs6733957
Chromosome Location	chr2:99359117-99359118
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	chr2:99358144..99360845-chr2:99364555..99366061,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1016124	0.81[EUR][1000 genomes]
rs10177696	0.88[EUR][1000 genomes]
rs10194177	0.87[EUR][1000 genomes]
rs10196218	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs10199267	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10460485	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10496332	0.81[EUR][1000 genomes]
rs11123747	0.81[EUR][1000 genomes]
rs11123749	0.81[EUR][1000 genomes]
rs12471383	0.81[EUR][1000 genomes]
rs12477450	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs12615301	0.81[EUR][1000 genomes]
rs12622931	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13391483	0.81[EUR][1000 genomes]
rs13391794	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428808	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1514916	0.88[EUR][1000 genomes]
rs1913621	0.81[EUR][1000 genomes]
rs28783173	0.81[EUR][1000 genomes]
rs41445250	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4851150	0.81[EUR][1000 genomes]
rs4851154	0.81[EUR][1000 genomes]
rs58666702	0.88[EUR][1000 genomes]
rs60024860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706340	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6729151	0.83[EUR][1000 genomes]
rs6737760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740656	0.83[EUR][1000 genomes]
rs6751196	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7420869	0.83[EUR][1000 genomes]
rs7558236	0.81[EUR][1000 genomes]
rs7577636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7599792	0.81[EUR][1000 genomes]
rs7601040	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6733957	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
2	chr2:99348600-99359200	Weak transcription	Aorta	Aorta
3	chr2:99348800-99360600	Weak transcription	Lung	lung
4	chr2:99351800-99360400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:99351800-99360600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:99352800-99360400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:99353400-99359400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:99353400-99360400	Weak transcription	HMEC	breast
9	chr2:99353600-99359400	Weak transcription	HUVEC	blood vessel
10	chr2:99354000-99359400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:99354600-99359200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:99354600-99359600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:99354600-99364600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr2:99354800-99360600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:99354800-99364000	Weak transcription	Dnd41	blood
16	chr2:99355000-99359200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:99355000-99359200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:99355000-99362200	Weak transcription	Thymus	Thymus
19	chr2:99355200-99359200	Weak transcription	Gastric	stomach
20	chr2:99355200-99359400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:99355200-99360800	Weak transcription	Small Intestine	intestine
22	chr2:99355600-99359200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:99355600-99359600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:99355800-99359200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:99355800-99359200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:99355800-99359200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:99355800-99359400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:99356000-99359400	Weak transcription	Primary T cells from cord blood	blood
29	chr2:99356200-99359200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:99356600-99360000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:99357200-99361000	Weak transcription	HepG2	liver
32	chr2:99357400-99359200	Weak transcription	Left Ventricle	heart
33	chr2:99357400-99359200	Weak transcription	Pancreas	Pancrea
34	chr2:99357400-99360000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:99358600-99361400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:99359000-99359600	Enhancers	Placenta	Placenta

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