Variant report

Variant	rs17302408
Chromosome Location	chr5:14283073-14283074
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14279019..14280717-chr5:14281044..14283924,2	K562	blood:
2	chr5:14142997..14144826-chr5:14282663..14285060,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11747048	1.00[CHB][hapmap]
rs13175673	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13177026	0.83[AFR][1000 genomes]
rs13184211	1.00[CHB][hapmap]
rs13184670	1.00[CHB][hapmap]
rs164861	1.00[ASN][1000 genomes]
rs17299045	1.00[CHB][hapmap]
rs187125	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs2434605	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs245577	1.00[ASN][1000 genomes]
rs26057	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs26058	1.00[CHB][hapmap]
rs26059	1.00[CHB][hapmap]
rs26061	1.00[CHB][hapmap]
rs2607077	1.00[ASN][1000 genomes]
rs2607078	1.00[ASN][1000 genomes]
rs2697663	1.00[ASN][1000 genomes]
rs27665	1.00[CHB][hapmap]
rs28010	1.00[CHB][hapmap]
rs30616	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30617	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs30619	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs30620	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs32339	1.00[CHB][hapmap]
rs32341	1.00[CHB][hapmap]
rs32390	1.00[CHB][hapmap]
rs32394	1.00[CHB][hapmap]
rs34045422	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs354285	1.00[CHB][hapmap]
rs354298	1.00[CHB][hapmap]
rs354300	1.00[CHB][hapmap]
rs354305	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs354308	1.00[ASN][1000 genomes]
rs354312	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs3849082	1.00[CHB][hapmap]
rs39856	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs42485	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702028	1.00[CHB][hapmap]
rs706271	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs71614082	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs773701	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs773702	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs773703	1.00[CHB][hapmap]
rs773763	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs799025	1.00[ASN][1000 genomes]
rs897724	1.00[ASN][1000 genomes]
rs897726	1.00[ASN][1000 genomes]
rs923616	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17302408	MARCH6	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14265200-14293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:14265400-14284600	Weak transcription	Stomach Mucosa	stomach
3	chr5:14265400-14286600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:14268600-14291000	Weak transcription	Fetal Kidney	kidney
5	chr5:14269200-14286400	Weak transcription	Pancreas	Pancrea
6	chr5:14269200-14286600	Weak transcription	Spleen	Spleen
7	chr5:14270200-14290800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:14270400-14283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:14270400-14284400	Weak transcription	Colonic Mucosa	Colon
10	chr5:14270400-14284600	Weak transcription	Brain Germinal Matrix	brain
11	chr5:14270400-14284800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:14270400-14284800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:14270400-14286400	Weak transcription	Fetal Intestine Small	intestine
14	chr5:14270400-14286800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:14270400-14288800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:14270400-14289400	Weak transcription	Gastric	stomach
17	chr5:14270400-14293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:14270400-14305200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:14270400-14313600	Weak transcription	Small Intestine	intestine
20	chr5:14270800-14286800	Weak transcription	Fetal Brain Male	brain
21	chr5:14270800-14293000	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:14271000-14295800	Weak transcription	Brain Angular Gyrus	brain
23	chr5:14271800-14284400	Weak transcription	Aorta	Aorta
24	chr5:14273600-14284200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:14276600-14284600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:14276800-14290800	Weak transcription	Esophagus	oesophagus
27	chr5:14277200-14291000	Weak transcription	Brain Anterior Caudate	brain
28	chr5:14277800-14284600	Weak transcription	Primary T cells from cord blood	blood
29	chr5:14277800-14286800	Weak transcription	Brain Substantia Nigra	brain
30	chr5:14278000-14284600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:14278000-14341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:14278400-14284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:14278600-14284400	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:14278600-14284800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:14278600-14285800	Strong transcription	HSMM	muscle
36	chr5:14278600-14296200	Strong transcription	NH-A	brain
37	chr5:14279200-14285400	Strong transcription	Primary B cells from cord blood	blood
38	chr5:14279400-14284200	Strong transcription	NHDF-Ad	bronchial
39	chr5:14279600-14284000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:14279600-14284600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:14279600-14284800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:14279600-14285000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr5:14279600-14295600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:14279800-14283800	Genic enhancers	Left Ventricle	heart
45	chr5:14279800-14284200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr5:14279800-14285200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:14279800-14287800	Enhancers	Fetal Heart	heart
48	chr5:14279800-14287800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr5:14279800-14293200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:14279800-14294600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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