Variant report

Variant	rs4700813
Chromosome Location	chr5:179037989-179037990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:178976906..178979400-chr5:179037284..179038987,2	K562	blood:
2	chr5:178977556..178979400-chr5:179037487..179040033,2	K562	blood:
3	chr5:179037627..179040262-chr5:179091207..179093202,2	K562	blood:
4	chr5:179012467..179014455-chr5:179037577..179039741,2	K562	blood:
5	chr5:179036525..179040506-chr5:179125503..179127596,3	K562	blood:
6	chr5:179034167..179038139-chr5:179125249..179127406,3	MCF-7	breast:
7	chr5:178982934..178985451-chr5:179036566..179039640,3	K562	blood:
8	chr5:179037382..179039814-chr5:179164191..179166934,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000176783	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs4331859	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs4364351	0.85[CHB][hapmap]
rs4700817	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4701135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58828813	0.91[ASN][1000 genomes]
rs6886107	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs72822602	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72824510	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72824515	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72824520	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824522	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824524	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824531	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72824532	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824544	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72824556	0.84[ASN][1000 genomes]
rs73809617	0.82[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	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4700813	HNRNPH1	cis	parietal	SCAN
rs4700813	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs4700813	RAB24	cis	parietal	SCAN
rs4700813	CLTB	cis	parietal	SCAN
rs4700813	UNC5A	cis	cerebellum	SCAN
rs4700813	BTNL3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178987200-179040800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:178987600-179045600	Strong transcription	Fetal Intestine Small	intestine
3	chr5:178987800-179045600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:179002200-179045600	Strong transcription	Fetal Intestine Large	intestine
5	chr5:179007400-179040200	Strong transcription	Placenta	Placenta
6	chr5:179007400-179045000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:179011000-179045600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:179011200-179039000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:179011200-179043800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:179012600-179047000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr5:179012800-179039000	Strong transcription	Left Ventricle	heart
12	chr5:179012800-179040000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr5:179013800-179044800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:179014000-179042000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:179014000-179044400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:179014000-179046000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:179016000-179041800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:179016200-179045000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr5:179025200-179045000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:179026600-179040600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:179027600-179039600	Weak transcription	Small Intestine	intestine
22	chr5:179028200-179046200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr5:179028400-179046000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr5:179028600-179046200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:179028800-179045000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr5:179029000-179038800	Strong transcription	Fetal Lung	lung
27	chr5:179029200-179045600	Strong transcription	Primary B cells from cord blood	blood
28	chr5:179030000-179040800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:179031000-179041000	Genic enhancers	Fetal Muscle Leg	muscle
30	chr5:179031000-179045600	Strong transcription	Osteobl	bone
31	chr5:179031000-179046200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr5:179032200-179038800	Strong transcription	Pancreas	Pancrea
33	chr5:179032200-179039200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr5:179032200-179045800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:179032200-179046400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:179032400-179038400	Strong transcription	HepG2	liver
37	chr5:179032400-179039800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:179032400-179045600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:179032400-179047400	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr5:179032600-179038600	Strong transcription	Liver	Liver
41	chr5:179032800-179045000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:179033600-179046000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr5:179034000-179038000	Genic enhancers	Fetal Thymus	thymus
44	chr5:179034200-179046600	Strong transcription	Colonic Mucosa	Colon
45	chr5:179034400-179038200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:179034600-179039200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:179034600-179039200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr5:179034600-179043000	Weak transcription	Right Atrium	heart
49	chr5:179035000-179038800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:179035000-179043000	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links