Variant report

Variant	rs2499856
Chromosome Location	chr1:161926637-161926638
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	chr1:161925023..161927018-chr1:161928283..161930641,2	K562	blood:
2	chr1:161924382..161927245-chr1:161933374..161935205,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10733044	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737502	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753645	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753666	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800068	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394070	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553444	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134690	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2134696	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2298019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341468	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2341479	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880055	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312480	1.00[ASN][1000 genomes]
rs34461550	0.90[ASN][1000 genomes]
rs35621393	0.94[ASN][1000 genomes]
rs36080602	1.00[ASN][1000 genomes]
rs3767633	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233380	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300199	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579731	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4656335	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656339	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6427633	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427639	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667896	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685369	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6698065	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs71639910	0.98[ASN][1000 genomes]
rs7517386	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532448	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924777	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1007108	chr1:161925814-162002917	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161824200-161928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:161861600-161936000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:161883400-161928200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:161884600-161927600	Weak transcription	NHEK	skin
5	chr1:161885000-161928000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:161887000-161928200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:161887200-161929600	Weak transcription	Hela-S3	cervix
8	chr1:161897800-161928400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:161897800-161940000	Weak transcription	Brain Germinal Matrix	brain
10	chr1:161901400-161935400	Weak transcription	Fetal Lung	lung
11	chr1:161902800-161943400	Weak transcription	Esophagus	oesophagus
12	chr1:161903600-161930400	Weak transcription	Fetal Brain Female	brain
13	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
14	chr1:161906000-161927800	Weak transcription	Thymus	Thymus
15	chr1:161906800-161928000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:161906800-161932200	Weak transcription	Stomach Mucosa	stomach
17	chr1:161911000-161937200	Weak transcription	Gastric	stomach
18	chr1:161911600-161939400	Weak transcription	HepG2	liver
19	chr1:161912600-161941600	Weak transcription	Fetal Kidney	kidney
20	chr1:161912800-161927800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:161913600-161928000	Weak transcription	Fetal Intestine Large	intestine
22	chr1:161913600-161931600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:161914000-161932000	Weak transcription	Aorta	Aorta
24	chr1:161914600-161927800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:161914600-161927800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:161914800-161928000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:161914800-161928000	Weak transcription	Placenta	Placenta
28	chr1:161915000-161928400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:161915000-161930800	Weak transcription	HUVEC	blood vessel
30	chr1:161915200-161928200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:161916200-161927600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:161916200-161927800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:161916200-161927800	Weak transcription	Pancreas	Pancrea
34	chr1:161916200-161930400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:161916200-161935600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:161916800-161931200	Weak transcription	HSMMtube	muscle
37	chr1:161917200-161928000	Weak transcription	Ovary	ovary
38	chr1:161917200-161928000	Weak transcription	Spleen	Spleen
39	chr1:161919400-161927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:161919600-161930800	Weak transcription	Psoas Muscle	Psoas
41	chr1:161922800-161928400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:161923000-161926800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:161923000-161927200	Enhancers	Fetal Muscle Leg	muscle
44	chr1:161923400-161927200	Enhancers	NHLF	lung
45	chr1:161923600-161928200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:161923800-161928000	Weak transcription	GM12878-XiMat	blood
47	chr1:161924000-161927400	Weak transcription	Dnd41	blood
48	chr1:161924000-161931000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:161924200-161927600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:161924200-161927600	Weak transcription	Brain Inferior Temporal Lobe	brain

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