Variant report

Variant	rs1009742
Chromosome Location	chr6:80399438-80399439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1883878	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473826	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2746314	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2746317	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812701	0.88[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2812703	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812708	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812712	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2812713	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927296	1.00[JPT][hapmap]
rs980225	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80373400-80412400	Weak transcription	Fetal Brain Male	brain
2	chr6:80376400-80402000	Weak transcription	Brain Substantia Nigra	brain
3	chr6:80378200-80405000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:80378400-80403800	Weak transcription	Esophagus	oesophagus
5	chr6:80381600-80400600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:80381600-80408200	Weak transcription	Fetal Stomach	stomach
7	chr6:80382200-80411800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:80382600-80414800	Weak transcription	HUVEC	blood vessel
9	chr6:80382800-80413000	Weak transcription	Placenta	Placenta
10	chr6:80382800-80414000	Weak transcription	HSMM	muscle
11	chr6:80384200-80406200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:80384600-80405600	Weak transcription	Fetal Kidney	kidney
13	chr6:80396800-80399600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:80396800-80413600	Weak transcription	Ovary	ovary
15	chr6:80396800-80419800	Weak transcription	Right Ventricle	heart
16	chr6:80396800-80420000	Weak transcription	Lung	lung
17	chr6:80397000-80403600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:80397000-80403600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:80397000-80408800	Weak transcription	Left Ventricle	heart
20	chr6:80397600-80414400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:80397600-80416000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:80397800-80403400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:80397800-80403400	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:80397800-80403600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:80397800-80403600	Weak transcription	Psoas Muscle	Psoas
26	chr6:80397800-80404400	Weak transcription	Right Atrium	heart
27	chr6:80397800-80404800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:80397800-80407200	Weak transcription	Liver	Liver
29	chr6:80397800-80407400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:80397800-80409200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:80397800-80412000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:80397800-80414200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:80397800-80416000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:80397800-80421400	Weak transcription	Pancreas	Pancrea
35	chr6:80398000-80421400	Weak transcription	Stomach Mucosa	stomach
36	chr6:80398200-80403600	Weak transcription	Adipose Nuclei	Adipose
37	chr6:80398200-80409400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:80398200-80421400	Weak transcription	Fetal Lung	lung
39	chr6:80398400-80399600	Weak transcription	Fetal Intestine Small	intestine
40	chr6:80398400-80400000	Weak transcription	Fetal Intestine Large	intestine
41	chr6:80398400-80407000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:80398400-80407800	Weak transcription	HepG2	liver
43	chr6:80398400-80409600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:80398800-80404800	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links