Variant report

Variant	rs6787808
Chromosome Location	chr3:49079105-49079106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49064556..49067691-chr3:49076131..49079895,4	K562	blood:

Variant related genes	Relation type
ENSG00000272434	Chromatin interaction
ENSG00000178035	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10154992	0.86[CEU][hapmap]
rs11130183	0.82[CEU][hapmap]
rs13084037	1.00[YRI][hapmap]
rs3087866	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs4292260	0.95[CEU][hapmap]
rs4955411	0.95[CEU][hapmap]
rs4955416	1.00[CEU][hapmap]
rs4955426	0.95[CEU][hapmap]
rs4955439	0.82[CEU][hapmap]
rs4974081	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4974083	1.00[CEU][hapmap]
rs4974088	1.00[CEU][hapmap]
rs6446204	1.00[CEU][hapmap]
rs6446256	0.86[CEU][hapmap]
rs6446257	0.81[CEU][hapmap]
rs6769821	0.82[CEU][hapmap]
rs6772452	1.00[CEU][hapmap]
rs6798112	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7100	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs7373072	1.00[CEU][hapmap]
rs7429661	0.82[CEU][hapmap]
rs7434187	1.00[CEU][hapmap]
rs7619016	0.86[CEU][hapmap]
rs7621226	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7653408	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9284885	1.00[CEU][hapmap]
rs9834003	0.82[CEU][hapmap]
rs9864243	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs9865051	0.95[CEU][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6787808	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6787808	AMT	cis	Artery Aorta	GTEx
rs6787808	AMT	cis	Thyroid	GTEx
rs6787808	NICN1-AS1	cis	Thyroid	GTEx
rs6787808	AMT	cis	Nerve Tibial	GTEx
rs6787808	AMT	cis	Artery Tibial	GTEx
rs6787808	AMT	cis	lung	GTEx
rs6787808	WDR6	cis	Nerve Tibial	GTEx
rs6787808	NICN1	cis	Thyroid	GTEx
rs6787808	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6787808	AMT	cis	Whole Blood	GTEx
rs6787808	WDR6	cis	Muscle Skeletal	GTEx
rs6787808	ARIH2	cis	Thyroid	GTEx
rs6787808	AMT	cis	Adipose Subcutaneous	GTEx
rs6787808	P4HTM	cis	lung	GTEx
rs6787808	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6787808	QRICH1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49067200-49085600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
5	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:49067400-49079800	Strong transcription	Placenta	Placenta
7	chr3:49067400-49085000	Strong transcription	Brain Germinal Matrix	brain
8	chr3:49067400-49085600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:49067400-49085600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:49067400-49085600	Strong transcription	Fetal Intestine Large	intestine
11	chr3:49067400-49086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:49067400-49086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:49067400-49090000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
17	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
18	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
19	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:49067600-49080200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:49067600-49085600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:49067600-49085600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:49067600-49085600	Strong transcription	Liver	Liver
25	chr3:49067600-49086600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:49067600-49086800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:49067600-49095800	Strong transcription	Dnd41	blood
28	chr3:49067600-49097000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
30	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:49067800-49086800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:49067800-49086800	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:49068200-49081200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:49070600-49079800	Weak transcription	A549	lung
36	chr3:49070600-49085000	Strong transcription	Adipose Nuclei	Adipose
37	chr3:49070800-49079600	Weak transcription	Esophagus	oesophagus
38	chr3:49070800-49083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:49070800-49084600	Strong transcription	Fetal Lung	lung
40	chr3:49070800-49085600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:49070800-49085600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:49070800-49085800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:49070800-49117000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:49071000-49080000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:49071000-49080200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:49071000-49081200	Weak transcription	Pancreas	Pancrea
47	chr3:49071000-49083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:49071000-49083800	Weak transcription	NHLF	lung
49	chr3:49071200-49082000	Weak transcription	Fetal Heart	heart
50	chr3:49071600-49086600	Strong transcription	Osteobl	bone

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