Variant report

Variant	rs10205639
Chromosome Location	chr2:50719564-50719565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:50629632..50630141-chr2:50719329..50719849,2	MCF-7	breast:
2	chr2:48772065..48772805-chr2:50719351..50720113,2	K562	blood:
3	chr2:50571653..50572272-chr2:50719383..50719965,2	MCF-7	breast:
4	chr2:50551521..50552446-chr2:50719322..50720205,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10165207	1.00[EUR][1000 genomes]
rs10165473	1.00[EUR][1000 genomes]
rs10168312	1.00[EUR][1000 genomes]
rs10169577	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10170613	1.00[AMR][1000 genomes]
rs10177472	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10181113	1.00[EUR][1000 genomes]
rs10181317	0.91[YRI][hapmap]
rs10190049	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10194089	1.00[AMR][1000 genomes]
rs10200688	0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211401	1.00[AMR][1000 genomes]
rs10221724	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10221944	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125307	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125308	1.00[AMR][1000 genomes]
rs11125309	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125310	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125312	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125313	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13398501	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13402154	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13402266	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13402450	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13409159	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13409894	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13410477	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13411836	1.00[AMR][1000 genomes]
rs13411953	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420978	1.00[AMR][1000 genomes]
rs13423536	1.00[AMR][1000 genomes]
rs13423656	1.00[AMR][1000 genomes]
rs13423870	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13424060	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13424091	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040790	1.00[AMR][1000 genomes]
rs28537655	1.00[EUR][1000 genomes]
rs28589462	1.00[EUR][1000 genomes]
rs28631421	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28684765	1.00[EUR][1000 genomes]
rs61331194	1.00[EUR][1000 genomes]
rs6720227	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6722766	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6722905	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6723039	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6735456	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6735458	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745627	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7598865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv532650	chr2:50675808-51136752	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv491644	chr2:50680795-50892906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv498102	chr2:50680795-50937503	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv2724	chr2:50688876-50734321	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv532651	chr2:50712339-50758351	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv532681	chr2:50715261-51172182	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50699000-50742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:50717800-50719600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr2:50717800-50724000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:50718200-50719600	Enhancers	NHEK	skin
5	chr2:50718200-50719800	Enhancers	HMEC	breast
6	chr2:50718400-50719800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr2:50718600-50719600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:50718600-50719600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:50718600-50719600	Enhancers	Brain Germinal Matrix	brain
10	chr2:50718600-50719600	Enhancers	Fetal Brain Male	brain
11	chr2:50718600-50719600	Enhancers	Fetal Heart	heart
12	chr2:50718600-50719600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:50718600-50719800	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:50719000-50719600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:50719000-50719600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:50719000-50719600	Enhancers	Brain Substantia Nigra	brain
17	chr2:50719000-50719600	Enhancers	Fetal Brain Female	brain
18	chr2:50719000-50719800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:50719000-50719800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:50719200-50719600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:50719200-50719600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr2:50719200-50719600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:50719200-50719600	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr2:50719200-50719600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:50719200-50719600	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr2:50719200-50719600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:50719200-50719600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr2:50719200-50719600	Enhancers	Fetal Lung	lung
29	chr2:50719200-50719600	Enhancers	Placenta	Placenta
30	chr2:50719200-50719600	Flanking Active TSS	Stomach Mucosa	stomach
31	chr2:50719200-50719800	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr2:50719200-50719800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:50719200-50719800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr2:50719200-50719800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:50719200-50719800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:50719200-50719800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:50719200-50719800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:50719200-50719800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:50719200-50719800	Enhancers	Fetal Kidney	kidney
40	chr2:50719200-50719800	Enhancers	Dnd41	blood
41	chr2:50719400-50719600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:50719400-50719600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr2:50719400-50719600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr2:50719400-50719600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:50719400-50719600	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr2:50719400-50719600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr2:50719400-50719600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr2:50719400-50719600	Enhancers	Pancreas	Pancrea
49	chr2:50719400-50719600	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:50719400-50719600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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