Variant report

Variant	rs10216949
Chromosome Location	chr8:119047546-119047547
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:119039290..119041869-chr8:119044899..119048314,3	MCF-7	breast:
2	chr8:119046491..119049181-chr8:119099094..119101026,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAMD12-5	chr8:119047209-119047786	NONHSAT128403

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10088107	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10088828	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10095646	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10099230	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10104745	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10105934	0.91[ASN][1000 genomes]
rs10106128	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1020916	0.96[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10505325	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10955850	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10955851	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs10955852	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs11562725	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11562727	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11562814	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs1188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12541849	0.82[EUR][1000 genomes]
rs12544344	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13264371	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs13271950	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13277304	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13277610	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13282822	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2100617	0.82[EUR][1000 genomes]
rs2124959	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4876399	0.89[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6990802	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs6997001	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7004377	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73325947	0.88[EUR][1000 genomes]
rs7357466	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7357586	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7357588	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7813805	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7819492	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7829981	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7832327	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7833710	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs881989	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9649944	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9650073	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][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	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv831440	chr8:118871930-119052269	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1015380	chr8:118948652-119418389	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv539736	chr8:118948652-119418389	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1025002	chr8:118970940-119069418	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119039200-119049000	Weak transcription	HUVEC	blood vessel
2	chr8:119040600-119052600	Weak transcription	Left Ventricle	heart
3	chr8:119041400-119049800	Enhancers	NHDF-Ad	bronchial
4	chr8:119041800-119049800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:119042400-119052000	Weak transcription	Adipose Nuclei	Adipose
6	chr8:119043000-119048400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr8:119043200-119048400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:119043200-119050800	Enhancers	HMEC	breast
9	chr8:119043400-119054400	Weak transcription	Colon Smooth Muscle	Colon
10	chr8:119043400-119054400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:119044200-119049000	Weak transcription	HepG2	liver
12	chr8:119044400-119051200	Weak transcription	Fetal Kidney	kidney
13	chr8:119044600-119049400	Weak transcription	Liver	Liver
14	chr8:119044600-119056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr8:119044800-119048400	Weak transcription	Fetal Intestine Small	intestine
16	chr8:119044800-119053000	Weak transcription	Fetal Intestine Large	intestine
17	chr8:119045000-119047800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr8:119045800-119048000	Enhancers	Aorta	Aorta
19	chr8:119046200-119048600	Enhancers	A549	lung
20	chr8:119046400-119047600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr8:119046400-119047600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:119046400-119047600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:119046400-119051200	Enhancers	NHLF	lung
24	chr8:119046600-119047600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr8:119046600-119047600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr8:119046600-119047600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr8:119046600-119047600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:119046600-119047600	Enhancers	Esophagus	oesophagus
29	chr8:119046600-119047600	Enhancers	Fetal Muscle Leg	muscle
30	chr8:119046600-119047600	Enhancers	Pancreas	Pancrea
31	chr8:119046600-119047600	Enhancers	Rectal Smooth Muscle	rectum
32	chr8:119046600-119048600	Enhancers	Fetal Lung	lung
33	chr8:119046600-119049200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr8:119046600-119049200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr8:119046600-119049400	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr8:119046600-119049600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr8:119046600-119051000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr8:119046800-119047600	Enhancers	Fetal Brain Female	brain
39	chr8:119046800-119047600	Enhancers	Lung	lung
40	chr8:119046800-119047600	Enhancers	Ovary	ovary
41	chr8:119046800-119047600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr8:119046800-119049600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr8:119047000-119047600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr8:119047000-119047600	Enhancers	Stomach Smooth Muscle	stomach
45	chr8:119047000-119047800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:119047000-119047800	Enhancers	Osteobl	bone
47	chr8:119047000-119048400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr8:119047000-119049000	Weak transcription	Small Intestine	intestine
49	chr8:119047000-119049200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr8:119047000-119049400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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