Variant report

Variant	rs2506893
Chromosome Location	chr1:10599213-10599214
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10597953..10600122-chr1:10755934..10757500,2	K562	blood:
2	chr1:10594251..10596401-chr1:10598205..10601279,3	K562	blood:
3	chr1:10588129..10591030-chr1:10598382..10599942,2	K562	blood:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10779741	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10779742	0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11121586	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12562838	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128417	0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2480774	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2480776	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2480783	1.00[AMR][1000 genomes]
rs2506894	0.83[AFR][1000 genomes]
rs2506895	0.95[AFR][1000 genomes]
rs4593832	0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4846236	1.00[AMR][1000 genomes]
rs6540936	0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7512680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7527873	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7555010	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9659854	1.00[AMR][1000 genomes]
rs9662101	0.92[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:10584800-10603800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:10585200-10603600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:10585200-10603800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:10589000-10600000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
8	chr1:10590200-10602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:10590200-10605200	Weak transcription	NHDF-Ad	bronchial
10	chr1:10590600-10599400	Weak transcription	GM12878-XiMat	blood
11	chr1:10590800-10599800	Weak transcription	Right Ventricle	heart
12	chr1:10590800-10601000	Weak transcription	A549	lung
13	chr1:10591000-10600200	Weak transcription	HUVEC	blood vessel
14	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
15	chr1:10591200-10601000	Weak transcription	Placenta	Placenta
16	chr1:10591200-10601400	Weak transcription	Colonic Mucosa	Colon
17	chr1:10591400-10599600	Weak transcription	Fetal Kidney	kidney
18	chr1:10591400-10599600	Weak transcription	Ovary	ovary
19	chr1:10591400-10609000	Weak transcription	Small Intestine	intestine
20	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:10591600-10599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:10591600-10616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:10592000-10599600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:10592200-10615800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:10592800-10599800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:10593000-10599400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:10593000-10599800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:10593000-10603800	Weak transcription	Fetal Brain Female	brain
29	chr1:10593200-10599600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:10593400-10599400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:10593400-10599600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:10593400-10601000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:10593400-10603600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:10594600-10604400	Strong transcription	Fetal Intestine Small	intestine
35	chr1:10595000-10599800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:10595000-10600800	Weak transcription	HMEC	breast
37	chr1:10595600-10602400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:10595800-10602000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:10595800-10602400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:10595800-10603000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:10596000-10602200	Strong transcription	Primary T cells from cord blood	blood
42	chr1:10596000-10602600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:10596000-10602600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:10596200-10602400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:10596200-10602600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:10596400-10599400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:10596400-10603200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:10596800-10601000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:10596800-10601400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:10596800-10601400	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links