Variant report

Variant	rs6508781
Chromosome Location	chr19:38785318-38785319
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38784964..38786694-chr19:38794356..38796889,2	K562	blood:
2	chr19:38752235..38756779-chr19:38783718..38786830,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167644	Chromatin interaction
ENSG00000167642	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12610606	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610791	0.81[CHB][hapmap]
rs12983492	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs2060244	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2286475	0.82[ASW][hapmap]
rs34276782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34508901	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34992016	0.80[ASN][1000 genomes]
rs35029752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35366094	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745949	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3786874	0.82[YRI][hapmap]
rs71354994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7245454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253823	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254637	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259936	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73037326	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6508781	SLC1A5	cis	parietal	SCAN
rs6508781	CEACAM5	cis	parietal	SCAN
rs6508781	RPS16	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38765800-38794800	Weak transcription	Small Intestine	intestine
2	chr19:38769200-38791200	Weak transcription	Fetal Kidney	kidney
3	chr19:38769400-38795200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38770800-38785800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:38771400-38805800	Weak transcription	Right Atrium	heart
6	chr19:38773000-38785400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:38773000-38787800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:38773200-38785600	Strong transcription	Fetal Intestine Large	intestine
9	chr19:38774000-38785600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr19:38775800-38791000	Weak transcription	Liver	Liver
11	chr19:38777000-38791200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:38778000-38785400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:38778000-38785400	Genic enhancers	Placenta	Placenta
14	chr19:38778200-38785800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:38778400-38786000	Strong transcription	Aorta	Aorta
16	chr19:38778600-38786400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:38778800-38785400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:38778800-38785800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:38778800-38785800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:38779400-38785400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:38779400-38785400	Strong transcription	Spleen	Spleen
22	chr19:38779400-38785800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:38779600-38785600	Genic enhancers	NHEK	skin
24	chr19:38779800-38785400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:38779800-38789200	Weak transcription	Adipose Nuclei	Adipose
26	chr19:38780200-38785600	Genic enhancers	HMEC	breast
27	chr19:38781000-38794400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr19:38781200-38795800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:38781400-38795400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:38781400-38797800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:38781600-38785800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:38781600-38785800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr19:38781600-38789200	Weak transcription	Ovary	ovary
35	chr19:38781600-38795600	Weak transcription	Right Ventricle	heart
36	chr19:38781800-38787200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr19:38782200-38791200	Weak transcription	NHDF-Ad	bronchial
39	chr19:38782400-38798000	Weak transcription	Fetal Thymus	thymus
40	chr19:38782600-38796400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:38782800-38789200	Weak transcription	Gastric	stomach
42	chr19:38782800-38791200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:38782800-38791200	Weak transcription	Stomach Mucosa	stomach
44	chr19:38783000-38786400	Weak transcription	Fetal Brain Female	brain
45	chr19:38783000-38788800	Weak transcription	NHLF	lung
46	chr19:38783000-38789200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:38783000-38794200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:38783000-38795600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:38783200-38794200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:38783400-38797000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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