Variant report

Variant	rs9861342
Chromosome Location	chr3:112340843-112340844
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112338141..112343361-chr3:112351475..112354709,4	MCF-7	breast:
2	chr3:112340519..112345126-chr3:112357206..112361448,6	MCF-7	breast:
3	chr3:112340785..112342316-chr3:112345669..112347185,2	K562	blood:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10934178	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934179	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11712917	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1388443	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16859870	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16859871	0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4682418	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7349537	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7349538	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288955	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833212	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9851689	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870432	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881785	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
3	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:112318000-112341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112329600-112341800	Strong transcription	HSMM	muscle
6	chr3:112330400-112346800	Strong transcription	NHLF	lung
7	chr3:112331200-112351600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112331400-112354800	Weak transcription	Psoas Muscle	Psoas
9	chr3:112335200-112342200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:112335200-112345400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:112336000-112342000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:112336200-112342000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:112336200-112347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:112336200-112351600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:112336400-112341200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:112336400-112342000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:112336400-112346800	Weak transcription	Fetal Stomach	stomach
18	chr3:112336600-112351400	Weak transcription	Fetal Lung	lung
19	chr3:112336600-112355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:112337000-112346800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:112338000-112349400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:112338400-112346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:112338600-112341200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:112338600-112341800	Weak transcription	K562	blood
25	chr3:112338600-112342000	Strong transcription	NH-A	brain
26	chr3:112338600-112342200	Weak transcription	HUVEC	blood vessel
27	chr3:112338800-112341800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:112338800-112341800	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:112338800-112343600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:112339200-112341800	Strong transcription	Osteobl	bone
31	chr3:112339800-112341800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:112340000-112341000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:112340000-112341000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:112340000-112341000	Strong transcription	Aorta	Aorta
35	chr3:112340000-112341000	ZNF genes & repeats	A549	lung
36	chr3:112340000-112341400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:112340000-112341400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:112340000-112342200	Enhancers	Ovary	ovary
39	chr3:112340000-112342600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:112340000-112342800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:112340000-112343400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:112340200-112342000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:112340200-112342600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:112340200-112342800	Strong transcription	HSMMtube	muscle
45	chr3:112340600-112341000	Strong transcription	Fetal Kidney	kidney
46	chr3:112340600-112341200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:112340600-112341200	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr3:112340800-112341400	Genic enhancers	Adipose Nuclei	Adipose
49	chr3:112340800-112342000	Strong transcription	NHDF-Ad	bronchial
50	chr3:112340800-112348200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links