Variant report

Variant	rs3799638
Chromosome Location	chr6:166954602-166954603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11968034	1.00[JPT][hapmap]
rs16899101	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2344712	1.00[JPT][hapmap]
rs3778410	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3778414	1.00[ASN][1000 genomes]
rs3778416	1.00[JPT][hapmap]
rs3799640	1.00[ASN][1000 genomes]
rs3799642	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3799645	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6456087	0.82[JPT][hapmap]
rs763187	0.89[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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:166929600-166955600	Weak transcription	HMEC	breast
3	chr6:166930400-166957800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:166935400-166966400	Weak transcription	NH-A	brain
5	chr6:166938200-166955800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:166941400-166955600	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:166941800-166954800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:166944200-166954800	Weak transcription	Stomach Mucosa	stomach
9	chr6:166944400-166954800	Weak transcription	Colonic Mucosa	Colon
10	chr6:166944600-166955600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:166944600-166957200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:166944600-166958600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:166947200-166955000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:166947400-166969400	Weak transcription	Aorta	Aorta
15	chr6:166949600-166954800	Weak transcription	Pancreas	Pancrea
16	chr6:166949800-166955800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:166949800-166955800	Weak transcription	NHLF	lung
18	chr6:166949800-166956800	Weak transcription	Right Ventricle	heart
19	chr6:166949800-166964800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:166950000-166955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:166950200-166960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:166950800-166958600	Weak transcription	NHDF-Ad	bronchial
23	chr6:166951600-166955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:166951800-166959000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:166952000-166954800	Weak transcription	Ovary	ovary
26	chr6:166952000-166955400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:166952000-166955800	Weak transcription	HUVEC	blood vessel
28	chr6:166952000-166957000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:166952400-166957200	Weak transcription	Fetal Brain Male	brain
30	chr6:166952400-166969000	Weak transcription	Psoas Muscle	Psoas
31	chr6:166952800-166954800	Enhancers	Brain Cingulate Gyrus	brain
32	chr6:166952800-166955400	Weak transcription	Fetal Stomach	stomach
33	chr6:166953000-166955000	Enhancers	Brain Angular Gyrus	brain
34	chr6:166953000-166956200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:166953000-166956400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr6:166953000-166957800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:166953000-166959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:166953200-166954800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr6:166953200-166954800	Enhancers	Left Ventricle	heart
40	chr6:166953200-166955000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:166953200-166955000	Enhancers	Brain Substantia Nigra	brain
42	chr6:166953200-166956600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:166953400-166955200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr6:166953400-166955400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:166953400-166955600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:166953400-166955800	Enhancers	Brain Hippocampus Middle	brain
47	chr6:166953400-166957200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:166953400-166957600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr6:166953400-166964600	Weak transcription	Primary T cells from cord blood	blood
50	chr6:166953400-166967400	Weak transcription	Fetal Lung	lung

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