Variant report

Variant	rs41271807
Chromosome Location	chr6:25420350-25420351
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1028885	0.93[ASN][1000 genomes]
rs4712938	0.87[ASN][1000 genomes]
rs57541514	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58657257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59284567	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6900224	0.93[ASN][1000 genomes]
rs969645	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:25414600-25420400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:25414600-25423600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:25415000-25446200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:25415200-25420400	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25415200-25431800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:25415600-25421000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:25415600-25422400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:25415600-25424000	Weak transcription	Thymus	Thymus
10	chr6:25416200-25441000	Weak transcription	Fetal Thymus	thymus
11	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
12	chr6:25416600-25427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:25417600-25431800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:25418000-25421200	Weak transcription	Liver	Liver
16	chr6:25418000-25429200	Weak transcription	Aorta	Aorta
17	chr6:25418400-25420800	Weak transcription	Brain Substantia Nigra	brain
18	chr6:25418400-25422000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:25418600-25420400	Enhancers	Right Atrium	heart
20	chr6:25418600-25426200	Weak transcription	Gastric	stomach
21	chr6:25418800-25420400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:25418800-25420400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:25418800-25421600	Weak transcription	Adipose Nuclei	Adipose
24	chr6:25418800-25462600	Weak transcription	Ovary	ovary
25	chr6:25419000-25420800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr6:25419400-25420400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:25419400-25420400	Weak transcription	Fetal Lung	lung
28	chr6:25419400-25421000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr6:25419400-25421400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
30	chr6:25419400-25430600	Weak transcription	Left Ventricle	heart
31	chr6:25419600-25420800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
32	chr6:25419600-25421400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr6:25419800-25420600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr6:25419800-25420800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:25419800-25421400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:25419800-25429000	Weak transcription	Small Intestine	intestine
37	chr6:25420000-25421000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr6:25420000-25421400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:25420200-25420400	Weak transcription	Fetal Intestine Large	intestine
40	chr6:25420200-25420400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr6:25420200-25420600	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:25420200-25420800	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr6:25420200-25420800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:25420200-25420800	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr6:25420200-25421400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:25420200-25421400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:25420200-25421600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links