Variant report

Variant	rs2506896
Chromosome Location	chr1:10603716-10603717
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	chr1:10601514..10603833-chr1:10611610..10614031,2	K562	blood:
2	chr1:10595945..10600298-chr1:10602356..10606682,5	K562	blood:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11121587	0.98[EUR][1000 genomes]
rs12028449	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12375	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12741973	0.91[ASN][1000 genomes]
rs1411402	0.91[EUR][1000 genomes]
rs1632108	0.80[EUR][1000 genomes]
rs17035305	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2026792	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2056417	0.91[EUR][1000 genomes]
rs2150038	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2480777	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2480785	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2483677	0.91[EUR][1000 genomes]
rs2506880	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2506889	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2506892	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2847344	0.87[EUR][1000 genomes]
rs34575776	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845937	0.84[ASN][1000 genomes]
rs4846235	0.97[EUR][1000 genomes]
rs589400	0.80[EUR][1000 genomes]
rs596537	0.80[EUR][1000 genomes]
rs597438	0.80[EUR][1000 genomes]
rs616402	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs616488	0.81[AMR][1000 genomes]
rs617728	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs620405	0.80[EUR][1000 genomes]
rs622623	0.80[EUR][1000 genomes]
rs648324	0.80[EUR][1000 genomes]
rs648399	0.80[EUR][1000 genomes]
rs67488812	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs683864	0.80[EUR][1000 genomes]
rs9430149	0.80[AMR][1000 genomes];0.98[EUR][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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:10584800-10603800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:10585200-10603800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
5	chr1:10590200-10605200	Weak transcription	NHDF-Ad	bronchial
6	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
7	chr1:10591400-10609000	Weak transcription	Small Intestine	intestine
8	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:10591600-10616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:10592200-10615800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:10593000-10603800	Weak transcription	Fetal Brain Female	brain
12	chr1:10594600-10604400	Strong transcription	Fetal Intestine Small	intestine
13	chr1:10597200-10604800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:10598600-10621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:10599800-10608400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:10599800-10610000	Weak transcription	Stomach Mucosa	stomach
17	chr1:10600000-10608200	Weak transcription	Fetal Brain Male	brain
18	chr1:10600000-10615600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:10600000-10615800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:10600000-10619600	Weak transcription	Brain Substantia Nigra	brain
21	chr1:10600200-10614800	Weak transcription	Brain Angular Gyrus	brain
22	chr1:10600200-10615800	Weak transcription	HSMM	muscle
23	chr1:10601000-10604600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr1:10601000-10607600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:10601000-10613000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:10601200-10613400	Weak transcription	Osteobl	bone
27	chr1:10601200-10619600	Weak transcription	Brain Anterior Caudate	brain
28	chr1:10601400-10604600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:10601400-10604600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:10601400-10610400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:10601400-10611000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:10601400-10611000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:10601400-10615600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:10601600-10604400	Strong transcription	Fetal Stomach	stomach
35	chr1:10601600-10607000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:10601600-10607000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:10601800-10603800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:10601800-10605400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:10601800-10610000	Weak transcription	Fetal Lung	lung
40	chr1:10601800-10610000	Weak transcription	A549	lung
41	chr1:10601800-10610000	Weak transcription	HUVEC	blood vessel
42	chr1:10601800-10613200	Weak transcription	K562	blood
43	chr1:10601800-10613400	Weak transcription	Right Ventricle	heart
44	chr1:10602000-10603800	Weak transcription	Lung	lung
45	chr1:10602000-10606800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:10602000-10606800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:10602000-10607000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:10602000-10607000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:10602000-10607000	Weak transcription	Left Ventricle	heart
50	chr1:10602000-10607000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links