Variant report

Variant	rs3813630
Chromosome Location	chr1:161280249-161280250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:161280065-161280359	GM12878	blood:	n/a	chr1:161280243-161280256

No.	Distal block	Cell Line	Cell type
1	chr1:161278785..161280602-chr1:161282077..161284441,2	MCF-7	breast:
2	chr1:160989097..160992016-chr1:161278410..161280382,2	K562	blood:
3	chr1:161194292..161205045-chr1:161279588..161288493,17	K562	blood:

Variant related genes	Relation type
SDHC	TF binding region
MPZ	TF binding region
ENSG00000263548	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000158882	Chromatin interaction
ENSG00000143257	Chromatin interaction
ENSG00000143252	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11265586	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265587	0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12745115	0.91[ASN][1000 genomes]
rs12745664	0.89[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs34589411	0.91[ASN][1000 genomes]
rs4077630	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4282845	0.86[ASN][1000 genomes]
rs4656297	0.84[ASN][1000 genomes]
rs7530775	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3813630	NES	cis	parietal	SCAN
rs3813630	ISG20L2	cis	parietal	SCAN
rs3813630	RP11-122G18.5	cis	Muscle Skeletal	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161276000-161283800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:161276200-161283200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:161276200-161283600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:161276400-161282200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:161276400-161283400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:161276400-161283400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:161276400-161283400	Weak transcription	Liver	Liver
8	chr1:161276400-161283600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:161276600-161281200	Weak transcription	Fetal Kidney	kidney
10	chr1:161276600-161282800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:161276600-161283400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:161276600-161283400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:161276600-161283400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:161276600-161283400	Weak transcription	Right Atrium	heart
15	chr1:161276600-161283600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:161276800-161283400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:161276800-161283400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:161276800-161283400	Weak transcription	Brain Anterior Caudate	brain
19	chr1:161277000-161281000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:161277000-161283600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:161277200-161283000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:161277200-161283400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:161277200-161283400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:161277200-161283400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:161277200-161283400	Weak transcription	Esophagus	oesophagus
26	chr1:161277200-161283400	Weak transcription	Pancreas	Pancrea
27	chr1:161277200-161283400	Weak transcription	Spleen	Spleen
28	chr1:161277200-161283600	Weak transcription	Left Ventricle	heart
29	chr1:161277400-161281600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:161277400-161282400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:161277400-161283200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:161277400-161283200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:161277400-161283400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:161277400-161283400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:161277400-161283400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:161278200-161281000	Weak transcription	A549	lung
37	chr1:161278200-161283200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:161278200-161283200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:161278200-161283400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:161278200-161283400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:161278400-161283000	Weak transcription	Dnd41	blood
42	chr1:161278400-161283200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:161278400-161283200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:161278400-161283400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:161278400-161283400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:161278400-161283400	Weak transcription	HMEC	breast
47	chr1:161278600-161283400	Weak transcription	Hela-S3	cervix
48	chr1:161278800-161283400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:161278800-161283400	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:161278800-161283400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links