Variant report

Variant	rs4803238
Chromosome Location	chr19:39939991-39939992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39938346..39940025-chr19:39963736..39966601,2	MCF-7	breast:
2	chr19:39939856..39941421-chr19:40009261..40011843,2	K562	blood:

Variant related genes	Relation type
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10406924	0.84[ASN][1000 genomes]
rs10420073	0.85[EUR][1000 genomes]
rs10423921	0.84[EUR][1000 genomes]
rs10426543	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs11882744	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs1529733	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1865090	0.83[ASN][1000 genomes]
rs1865093	0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1865094	0.85[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs45568533	0.85[EUR][1000 genomes]
rs4802030	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs4802032	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs4802033	0.83[CHD][hapmap]
rs4803244	0.85[EUR][1000 genomes]
rs59269050	0.85[EUR][1000 genomes]
rs61480418	0.91[EUR][1000 genomes]
rs7245986	0.85[EUR][1000 genomes]
rs7246329	0.86[EUR][1000 genomes]
rs73035459	0.84[EUR][1000 genomes]
rs73035461	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
6	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4803238	CD177	cis	parietal	SCAN
rs4803238	B3GNT8	cis	parietal	SCAN
rs4803238	PRKD2	cis	cerebellum	SCAN
rs4803238	MIA	cis	cerebellum	SCAN
rs4803238	PHLDB3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39936800-39949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39937000-39949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39937200-39940600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:39937200-39941600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:39937200-39943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:39937400-39940000	Genic enhancers	Brain Cingulate Gyrus	brain
8	chr19:39937400-39940200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:39937400-39941200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:39937400-39942800	Weak transcription	Fetal Kidney	kidney
11	chr19:39937400-39944600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
13	chr19:39937600-39940000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:39937600-39940000	Enhancers	Liver	Liver
15	chr19:39937600-39940000	Genic enhancers	NHLF	lung
16	chr19:39937600-39940200	Genic enhancers	Brain Angular Gyrus	brain
17	chr19:39937600-39940200	Genic enhancers	K562	blood
18	chr19:39937600-39940400	Genic enhancers	Brain Germinal Matrix	brain
19	chr19:39937600-39946000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:39937600-39950000	Weak transcription	Fetal Brain Male	brain
21	chr19:39937800-39940000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:39937800-39940200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:39937800-39940600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
24	chr19:39937800-39941600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr19:39937800-39942200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:39937800-39943400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:39937800-39946200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:39938000-39940000	Genic enhancers	Dnd41	blood
29	chr19:39938000-39941800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr19:39938000-39942200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr19:39938200-39940000	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr19:39938200-39940600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:39938200-39942800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:39938400-39940000	Enhancers	Small Intestine	intestine
35	chr19:39938400-39940200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:39938400-39940200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:39938400-39940400	Genic enhancers	Primary T cells from cord blood	blood
38	chr19:39938400-39940400	Genic enhancers	Adipose Nuclei	Adipose
39	chr19:39938400-39941400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:39938400-39941400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:39938600-39940000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr19:39938600-39940000	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr19:39938600-39940000	Genic enhancers	Muscle Satellite Cultured Cells	--
44	chr19:39938600-39940200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
45	chr19:39938600-39940200	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr19:39938600-39940200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:39938600-39940200	Genic enhancers	Left Ventricle	heart
48	chr19:39938600-39940400	Genic enhancers	Pancreas	Pancrea
49	chr19:39938600-39940400	Genic enhancers	HepG2	liver
50	chr19:39938600-39941200	Genic enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links