Variant report

Variant	rs2688635
Chromosome Location	chr3:119371397-119371398
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	chr3:119367190..119369718-chr3:119370796..119372691,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12721613	1.00[MEX][hapmap]
rs1523128	1.00[MEX][hapmap]
rs1523129	1.00[MEX][hapmap]
rs1985121	0.88[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2472668	1.00[MEX][hapmap]
rs2670292	0.88[LWK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs2688643	1.00[MEX][hapmap]
rs2692619	1.00[MEX][hapmap]
rs4234663	1.00[MEX][hapmap]
rs4355316	1.00[MEX][hapmap]
rs4411917	1.00[MEX][hapmap]
rs4687883	1.00[MEX][hapmap]
rs4688038	1.00[MEX][hapmap]
rs524043	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs539627	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs541479	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs572119	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs575833	0.80[YRI][hapmap]
rs579196	0.85[AFR][1000 genomes]
rs6438543	1.00[MEX][hapmap]
rs940087	1.00[MEX][hapmap]
rs9816750	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
3	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
12	chr3:119358200-119372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:119358400-119376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:119358600-119371600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:119358600-119372400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:119358600-119376800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus
18	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:119361400-119372600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:119361400-119378800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:119362200-119371400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:119362400-119387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:119362600-119378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:119362600-119383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:119365200-119372200	Enhancers	Right Atrium	heart
28	chr3:119365200-119387400	Weak transcription	Liver	Liver
29	chr3:119367200-119375600	Weak transcription	GM12878-XiMat	blood
30	chr3:119367200-119378800	Weak transcription	Gastric	stomach
31	chr3:119367200-119381800	Weak transcription	Fetal Lung	lung
32	chr3:119367400-119371400	Weak transcription	Aorta	Aorta
33	chr3:119367400-119371400	Weak transcription	Fetal Stomach	stomach
34	chr3:119367400-119372800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:119367400-119375000	Weak transcription	Placenta	Placenta
36	chr3:119367400-119377800	Weak transcription	Fetal Intestine Small	intestine
37	chr3:119367400-119378000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:119367400-119378600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:119367400-119378800	Weak transcription	Pancreas	Pancrea
40	chr3:119367600-119371400	Weak transcription	Lung	lung
41	chr3:119367600-119378200	Weak transcription	Fetal Intestine Large	intestine
42	chr3:119367600-119389200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
44	chr3:119367800-119371400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:119367800-119371400	Weak transcription	Adipose Nuclei	Adipose
46	chr3:119367800-119371400	Weak transcription	Ovary	ovary
47	chr3:119367800-119378000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:119367800-119385400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:119367800-119386600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:119367800-119388800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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