Variant report

Variant	rs10036834
Chromosome Location	chr5:179454428-179454429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179452407..179455273-chr5:179474700..179476534,2	K562	blood:
2	chr5:179449447..179452303-chr5:179452707..179456164,4	K562	blood:
3	chr5:179246226..179248530-chr5:179451995..179454852,2	MCF-7	breast:
4	chr5:179449447..179452812-chr5:179452843..179455621,3	K562	blood:
5	chr5:179451009..179454455-chr5:179516109..179519066,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10061480	0.81[CEU][hapmap]
rs10068039	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10078977	0.81[CEU][hapmap]
rs10479557	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10903246	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12153541	0.96[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12653944	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs185076	0.81[CEU][hapmap]
rs248257	0.81[CEU][hapmap]
rs248258	0.81[CEU][hapmap]
rs248316	0.81[CEU][hapmap]
rs248319	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs27013	0.89[CEU][hapmap]
rs27014	0.81[CEU][hapmap]
rs27016	0.81[CEU][hapmap]
rs27019	0.81[CEU][hapmap]
rs394588	0.92[AFR][1000 genomes]
rs4130025	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4466125	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs449511	0.81[CEU][hapmap]
rs62405020	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6871596	0.92[AFR][1000 genomes]
rs6888883	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9329096	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10036834	LMAN2	cis	cerebellum	SCAN
rs10036834	TRIM7	cis	parietal	SCAN
rs10036834	RASGEF1C	cis	parietal	SCAN
rs10036834	RASGEF1C	cis	cerebellum	SCAN
rs10036834	FAM193B	cis	parietal	SCAN
rs10036834	ZFP2	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:179428600-179462200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr5:179429800-179462400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr5:179429800-179463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:179429800-179463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:179430600-179462400	Weak transcription	HepG2	liver
9	chr5:179435800-179454600	Weak transcription	K562	blood
10	chr5:179437600-179462600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:179438000-179466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:179440200-179457600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:179440200-179462600	Weak transcription	Fetal Intestine Large	intestine
14	chr5:179440600-179462400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:179446000-179462200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:179447600-179459600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:179447600-179462400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:179447600-179463200	Weak transcription	Esophagus	oesophagus
19	chr5:179447600-179463200	Weak transcription	Lung	lung
20	chr5:179447600-179463200	Weak transcription	HSMMtube	muscle
21	chr5:179447800-179454600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:179447800-179461600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:179447800-179461600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:179447800-179462400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:179447800-179462400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:179447800-179463000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:179447800-179463000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:179447800-179463200	Weak transcription	Ovary	ovary
29	chr5:179447800-179466800	Weak transcription	Hela-S3	cervix
30	chr5:179448000-179458600	Weak transcription	A549	lung
31	chr5:179448200-179457400	Weak transcription	Fetal Brain Female	brain
32	chr5:179448200-179459400	Weak transcription	Fetal Stomach	stomach
33	chr5:179448400-179461400	Weak transcription	Fetal Intestine Small	intestine
34	chr5:179448400-179461600	Weak transcription	Primary B cells from cord blood	blood
35	chr5:179449000-179454600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr5:179449000-179459400	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:179449000-179460200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:179449400-179462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:179450600-179466000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr5:179451000-179462600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr5:179451200-179460400	Weak transcription	Liver	Liver
42	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:179452200-179459400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:179452400-179454600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:179452400-179455200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:179452400-179463400	Weak transcription	Psoas Muscle	Psoas
47	chr5:179452600-179454600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:179452600-179454800	Enhancers	HUVEC	blood vessel
49	chr5:179452800-179454600	Enhancers	Brain Hippocampus Middle	brain
50	chr5:179452800-179455600	Enhancers	Brain Cingulate Gyrus	brain

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