Variant report

Variant	rs10205469
Chromosome Location	chr2:53926632-53926633
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53925981..53927589-chr2:53940700..53943084,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10168388	0.81[AFR][1000 genomes]
rs10179403	0.81[AFR][1000 genomes]
rs10180492	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10198317	1.00[CHD][hapmap]
rs10209918	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11125517	1.00[ASN][1000 genomes]
rs13382257	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13407905	0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs13408425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13432387	1.00[ASN][1000 genomes]
rs17045242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2177791	1.00[ASN][1000 genomes]
rs2177792	1.00[ASN][1000 genomes]
rs2287347	0.80[CEU][hapmap]
rs28391754	1.00[ASN][1000 genomes]
rs41536750	1.00[ASN][1000 genomes]
rs60769690	1.00[ASN][1000 genomes]
rs6545367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs6545368	0.80[CEU][hapmap]
rs6545369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6545372	1.00[ASN][1000 genomes]
rs6712561	1.00[ASN][1000 genomes]
rs6716978	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6739630	0.93[EUR][1000 genomes]
rs6740063	1.00[ASN][1000 genomes]
rs6745729	1.00[ASN][1000 genomes]
rs6759437	1.00[ASN][1000 genomes]
rs6760038	1.00[ASN][1000 genomes]
rs724387	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902931	1.00[ASN][1000 genomes]
rs73937421	1.00[ASN][1000 genomes]
rs7565152	1.00[ASN][1000 genomes]
rs7567225	1.00[ASN][1000 genomes]
rs7594327	1.00[ASN][1000 genomes]
rs7608085	1.00[ASN][1000 genomes]
rs7608989	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1009107	chr2:53896767-53946913	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014949	chr2:53896767-53947781	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1011400	chr2:53899956-53947781	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:53888200-53934200	Weak transcription	Lung	lung
4	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
5	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
6	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:53893800-53926800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:53896800-53936600	Weak transcription	Aorta	Aorta
10	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:53898200-53935400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:53898200-53935400	Weak transcription	Fetal Kidney	kidney
13	chr2:53900600-53935600	Weak transcription	K562	blood
14	chr2:53900800-53936400	Weak transcription	NH-A	brain
15	chr2:53900800-53936800	Weak transcription	NHLF	lung
16	chr2:53906600-53933800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:53906800-53935200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:53907200-53927000	Weak transcription	Placenta	Placenta
19	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
20	chr2:53909000-53934400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:53909000-53935200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:53910000-53935200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:53910000-53941600	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:53910600-53933600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:53911400-53935400	Weak transcription	Right Ventricle	heart
28	chr2:53911600-53936200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:53912400-53936200	Weak transcription	Gastric	stomach
30	chr2:53912600-53933600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:53912800-53927000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:53913000-53936200	Weak transcription	Spleen	Spleen
33	chr2:53914200-53934800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:53914600-53926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:53917600-53936200	Weak transcription	Esophagus	oesophagus
36	chr2:53917800-53934000	Weak transcription	Ovary	ovary
37	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
38	chr2:53919000-53935800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:53921600-53927000	Weak transcription	Brain Germinal Matrix	brain
40	chr2:53921800-53926800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:53921800-53933600	Weak transcription	Brain Anterior Caudate	brain
42	chr2:53921800-53933800	Weak transcription	Brain Angular Gyrus	brain
43	chr2:53921800-53935800	Weak transcription	Brain Substantia Nigra	brain
44	chr2:53922400-53935200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:53923400-53929400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:53924200-53926800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:53924200-53927600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:53924200-53927600	Strong transcription	Primary B cells from cord blood	blood
49	chr2:53924200-53927600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:53924200-53927600	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links