Variant report

Variant	rs10495256
Chromosome Location	chr1:227342798-227342799
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	chr1:227126988..227128747-chr1:227341911..227344210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10127638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10495257	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11582863	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11583489	0.82[CEU][hapmap]
rs12118840	1.00[JPT][hapmap]
rs12403775	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs1319103	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13376552	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1513609	0.87[AMR][1000 genomes]
rs1929855	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2813956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2953640	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs34111989	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3768420	0.81[CEU][hapmap]
rs3768437	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4146588	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs4653822	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6426578	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426584	1.00[JPT][hapmap]
rs66796195	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72748174	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72748192	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72748195	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72750169	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72750202	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72753628	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72755321	0.82[AMR][1000 genomes]
rs7355000	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7531992	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7540155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7540391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7553837	0.85[CEU][hapmap]
rs7553990	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs938257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
2	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
3	chr1:227288400-227343000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:227295200-227346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
7	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:227316600-227352200	Weak transcription	Gastric	stomach
9	chr1:227317000-227374200	Weak transcription	HepG2	liver
10	chr1:227323200-227346400	Weak transcription	Brain Substantia Nigra	brain
11	chr1:227324200-227348400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:227326600-227355200	Weak transcription	Small Intestine	intestine
13	chr1:227327000-227346200	Weak transcription	NH-A	brain
14	chr1:227327000-227346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:227327000-227347600	Weak transcription	Fetal Heart	heart
16	chr1:227327200-227348200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:227327200-227348200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:227328000-227354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:227328400-227350000	Weak transcription	Fetal Brain Male	brain
20	chr1:227328600-227351600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:227328800-227346200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:227328800-227354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:227329600-227358400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
25	chr1:227329800-227348400	Weak transcription	Fetal Brain Female	brain
26	chr1:227331400-227346200	Weak transcription	Pancreas	Pancrea
27	chr1:227331600-227355000	Weak transcription	Brain Anterior Caudate	brain
28	chr1:227331600-227358400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:227332200-227345800	Weak transcription	Fetal Stomach	stomach
30	chr1:227332400-227347400	Weak transcription	Fetal Intestine Small	intestine
31	chr1:227332800-227345800	Weak transcription	Left Ventricle	heart
32	chr1:227332800-227346000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:227332800-227346200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:227332800-227346200	Weak transcription	NHEK	skin
35	chr1:227332800-227346400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:227332800-227346400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:227332800-227350000	Weak transcription	HMEC	breast
38	chr1:227332800-227350200	Weak transcription	Lung	lung
39	chr1:227332800-227354600	Weak transcription	Ovary	ovary
40	chr1:227333000-227346000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:227333000-227346600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:227333000-227349400	Weak transcription	Placenta	Placenta
43	chr1:227333200-227354800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:227333400-227342800	Weak transcription	A549	lung
45	chr1:227333400-227344400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:227333400-227344400	Weak transcription	NHDF-Ad	bronchial
47	chr1:227333400-227344600	Weak transcription	HSMM	muscle
48	chr1:227333400-227345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:227333400-227346000	Weak transcription	Fetal Lung	lung
50	chr1:227333400-227346200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links