Variant report

Variant	rs1887460
Chromosome Location	chr10:112777889-112777890
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:112763502..112765745-chr10:112775415..112777948,2	MCF-7	breast:
2	chr10:112677980..112679509-chr10:112776501..112778401,2	MCF-7	breast:
3	chr10:112776495..112778257-chr10:112780884..112782883,2	K562	blood:

Variant related genes	Relation type
ENSG00000214413	Chromatin interaction
ENSG00000108061	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10787292	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10787298	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10885076	0.81[YRI][hapmap]
rs12412661	0.95[EUR][1000 genomes]
rs1327553	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359849	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1410054	0.91[ASN][1000 genomes]
rs1410055	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1410057	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1581886	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1980869	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4309090	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6585027	0.86[ASN][1000 genomes]
rs7082572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7085088	0.95[EUR][1000 genomes]
rs7086350	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7088364	0.91[ASN][1000 genomes]
rs7090695	0.95[EUR][1000 genomes]
rs7095404	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7101075	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs990429	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1048809	chr10:112683822-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1048444	chr10:112724159-112795159	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1036202	chr10:112726834-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1051595	chr10:112730022-112789048	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1047412	chr10:112747749-112781413	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112705200-112789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:112707200-112784200	Weak transcription	Left Ventricle	heart
3	chr10:112723200-112783000	Weak transcription	Small Intestine	intestine
4	chr10:112732600-112789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:112732800-112782800	Weak transcription	Esophagus	oesophagus
6	chr10:112732800-112789400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:112738000-112782800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:112738200-112784600	Weak transcription	Ovary	ovary
9	chr10:112738400-112779400	Weak transcription	HepG2	liver
10	chr10:112740400-112791800	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:112744800-112778800	Weak transcription	Hela-S3	cervix
12	chr10:112746000-112783400	Weak transcription	Colonic Mucosa	Colon
13	chr10:112746800-112782800	Weak transcription	Psoas Muscle	Psoas
14	chr10:112747400-112779800	Weak transcription	Fetal Brain Male	brain
15	chr10:112747600-112785200	Weak transcription	Fetal Brain Female	brain
16	chr10:112749200-112789400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:112750400-112785000	Weak transcription	A549	lung
18	chr10:112753200-112779200	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:112753200-112779600	Weak transcription	Brain Anterior Caudate	brain
20	chr10:112753200-112782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:112753200-112784200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:112753400-112789600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:112754000-112782000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:112754000-112784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:112754400-112782600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:112757200-112782400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr10:112758200-112783600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:112761600-112781400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr10:112761600-112782800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:112761800-112778200	Weak transcription	Fetal Intestine Small	intestine
31	chr10:112761800-112784200	Weak transcription	Spleen	Spleen
32	chr10:112762400-112780200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr10:112763000-112781600	Weak transcription	Brain Germinal Matrix	brain
34	chr10:112763400-112781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:112763600-112782400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr10:112764400-112783000	Weak transcription	Brain Substantia Nigra	brain
37	chr10:112764800-112778200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:112764800-112782600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr10:112765000-112781200	Weak transcription	Thymus	Thymus
40	chr10:112765000-112781800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:112765000-112782200	Weak transcription	Fetal Muscle Leg	muscle
42	chr10:112765000-112782400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr10:112765000-112782800	Weak transcription	Aorta	Aorta
44	chr10:112765000-112794200	Weak transcription	NH-A	brain
45	chr10:112765000-112794400	Weak transcription	NHLF	lung
46	chr10:112765200-112782600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr10:112765200-112794200	Weak transcription	NHEK	skin
48	chr10:112767600-112780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr10:112768600-112782200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr10:112769600-112780200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links