Variant report

Variant	rs6508755
Chromosome Location	chr19:38472722-38472723
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38420982..38422890-chr19:38471015..38472804,2	MCF-7	breast:
2	chr19:38421146..38425969-chr19:38469812..38473788,8	MCF-7	breast:
3	chr19:38471726..38473895-chr19:38475514..38478507,2	MCF-7	breast:
4	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
5	chr19:38417337..38419728-chr19:38472151..38473762,2	MCF-7	breast:
6	chr19:38429570..38433364-chr19:38470420..38473384,4	MCF-7	breast:
7	chr19:38464299..38466897-chr19:38471672..38473805,2	MCF-7	breast:
8	chr19:38469123..38470666-chr19:38472308..38474390,3	MCF-7	breast:
9	chr19:38394269..38398486-chr19:38470778..38473091,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1643455	1.00[CHB][hapmap]
rs1643459	1.00[CHB][hapmap]
rs17248670	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs17249336	1.00[CHB][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3859549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4536583	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55752822	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55785437	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55813548	0.83[AMR][1000 genomes]
rs55946812	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55974157	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55983118	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55994045	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56080901	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56207124	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56230664	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56246446	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56251160	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56252444	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56300335	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56676595	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs705501	1.00[CHB][hapmap]
rs7245855	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs7245962	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7257266	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258011	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73034922	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73036634	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73036658	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7343065	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap]
rs8100199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833905	1.00[CHB][hapmap]
rs833919	1.00[CHB][hapmap]
rs833920	1.00[CHB][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6508755	KIAA0961	cis	multi-tissue	Pritchard
rs6508755	AC012309.5	cis	Artery Tibial	GTEx
rs6508755	PLEKHG2	cis	cerebellum	SCAN
rs6508755	ZNF781	cis	Thyroid	GTEx
rs6508755	ARHGEF1	cis	cerebellum	SCAN
rs6508755	LYPD5	cis	cerebellum	SCAN
rs6508755	DMWD	cis	parietal	SCAN
rs6508755	ZNF226	cis	cerebellum	SCAN
rs6508755	TRAPPC6A	cis	cerebellum	SCAN
rs6508755	AC012309.5	cis	Thyroid	GTEx
rs6508755	AC012309.5	cis	Heart Left Ventricle	GTEx
rs6508755	AC012309.5	cis	Esophagus Mucosa	GTEx
rs6508755	C19orf61	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
8	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:38468200-38473600	Enhancers	Lung	lung
10	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:38468200-38475600	Enhancers	HMEC	breast
13	chr19:38468200-38475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:38468400-38473000	Enhancers	NH-A	brain
16	chr19:38468400-38473200	Enhancers	HSMM	muscle
17	chr19:38468800-38474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:38469000-38474200	Enhancers	Fetal Intestine Large	intestine
19	chr19:38469200-38474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:38469800-38475800	Genic enhancers	Fetal Intestine Small	intestine
22	chr19:38470000-38472800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr19:38470200-38473200	Enhancers	Fetal Lung	lung
24	chr19:38470200-38474200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr19:38470200-38474200	Enhancers	Stomach Mucosa	stomach
26	chr19:38470200-38474400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr19:38470400-38473600	Enhancers	Pancreas	Pancrea
28	chr19:38470400-38474400	Enhancers	Esophagus	oesophagus
29	chr19:38470400-38474800	Enhancers	Gastric	stomach
30	chr19:38470600-38473200	Enhancers	HSMMtube	muscle
31	chr19:38470600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:38470800-38473000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:38470800-38473600	Enhancers	Small Intestine	intestine
34	chr19:38470800-38474600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr19:38470800-38477200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
37	chr19:38471000-38472800	Enhancers	Fetal Kidney	kidney
38	chr19:38471000-38475400	Enhancers	NHEK	skin
39	chr19:38471000-38476800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr19:38471200-38472800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr19:38471200-38474600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr19:38471400-38473400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:38471400-38473400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:38471400-38473800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:38471400-38476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:38471400-38477000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:38471400-38483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:38471400-38488600	Weak transcription	NHLF	lung
50	chr19:38471600-38473000	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links