Variant report

Variant	rs13405165
Chromosome Location	chr2:208863429-208863430
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	chr2:208843739..208846333-chr2:208861565..208863915,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10176919	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10189041	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10195504	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10200892	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10209093	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10497889	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11692908	0.80[YRI][hapmap]
rs11895970	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11896789	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13392361	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13418213	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13422017	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13423906	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16840280	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2362781	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs59206831	0.88[AFR][1000 genomes]
rs59524824	0.92[AFR][1000 genomes]
rs6435400	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6707468	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6711353	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6715281	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73064902	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73066707	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73066710	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73066711	0.92[AFR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208834000-208864000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:208834800-208865000	Weak transcription	HSMMtube	muscle
3	chr2:208836000-208878400	Weak transcription	Fetal Kidney	kidney
4	chr2:208840000-208863800	Weak transcription	Placenta	Placenta
5	chr2:208841600-208864800	Weak transcription	HepG2	liver
6	chr2:208841600-208865200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:208841800-208864800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:208842000-208864200	Weak transcription	Fetal Thymus	thymus
9	chr2:208842200-208864200	Weak transcription	Fetal Brain Female	brain
10	chr2:208842200-208864200	Weak transcription	Fetal Lung	lung
11	chr2:208842200-208864400	Weak transcription	Brain Substantia Nigra	brain
12	chr2:208842200-208864400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:208842200-208864600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:208842200-208864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:208842200-208864800	Weak transcription	Aorta	Aorta
16	chr2:208842200-208864800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:208842200-208864800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:208842200-208864800	Weak transcription	Right Ventricle	heart
19	chr2:208842200-208865000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:208842200-208866600	Weak transcription	Gastric	stomach
21	chr2:208842200-208867600	Weak transcription	Thymus	Thymus
22	chr2:208842200-208871200	Weak transcription	Esophagus	oesophagus
23	chr2:208842400-208864200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:208842400-208864400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:208842400-208864800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:208842400-208866000	Weak transcription	Brain Germinal Matrix	brain
27	chr2:208842400-208867200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:208842400-208868200	Weak transcription	Dnd41	blood
29	chr2:208842600-208864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:208843600-208871200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:208848800-208864000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:208848800-208864200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:208848800-208864800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:208852200-208864800	Weak transcription	Spleen	Spleen
35	chr2:208852400-208864800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:208852400-208867200	Weak transcription	Psoas Muscle	Psoas
37	chr2:208852400-208868000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:208853800-208868000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:208854200-208889400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:208856400-208864600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:208856400-208864800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:208856600-208882000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:208857000-208864600	Weak transcription	Brain Anterior Caudate	brain
44	chr2:208857000-208864600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:208857000-208877200	Weak transcription	Pancreas	Pancrea
46	chr2:208857200-208888000	Weak transcription	Fetal Brain Male	brain
47	chr2:208857400-208864800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:208857600-208864400	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:208858000-208864800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:208858400-208864200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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