Variant report

Variant	rs2304132
Chromosome Location	chr19:38633159-38633160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38632809..38633724-chr19:38719989..38721047,3	K562	blood:
2	chr19:38629908..38632279-chr19:38632364..38634124,2	MCF-7	breast:
3	chr19:38632776..38633766-chr19:38724199..38724830,3	K562	blood:

Variant related genes	Relation type
ENSG00000011332	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10460171	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083447	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12460188	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12462587	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs12975576	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12984016	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12984380	0.86[EUR][1000 genomes]
rs12984864	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12985707	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1545039	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1962866	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2004981	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2010234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2016074	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2116862	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163817	0.93[EUR][1000 genomes]
rs2382972	0.90[EUR][1000 genomes]
rs2382973	0.91[EUR][1000 genomes]
rs2569517	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332841	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs332845	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332846	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332854	0.87[EUR][1000 genomes]
rs332857	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332859	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332860	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332861	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332862	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs332863	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34646932	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35467693	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35469521	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35972455	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3852910	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3852911	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802248	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803805	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803808	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67910767	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71337549	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7253312	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253633	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7258019	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8100956	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8107385	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855617	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];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	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
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2304132	MEGF8	cis	parietal	SCAN
rs2304132	EGLN2	cis	cerebellum	SCAN
rs2304132	MARK4	cis	cerebellum	SCAN
rs2304132	ERF	cis	cerebellum	SCAN
rs2304132	PAPL	cis	cerebellum	SCAN
rs2304132	LIPE	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
2	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
3	chr19:38610800-38643600	Weak transcription	HepG2	liver
4	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:38611600-38634400	Weak transcription	Stomach Mucosa	stomach
6	chr19:38611600-38634800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:38611600-38634800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:38611600-38641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
10	chr19:38611800-38634600	Weak transcription	NH-A	brain
11	chr19:38611800-38642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
13	chr19:38613400-38633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:38613400-38634400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:38613600-38634800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr19:38613800-38633400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:38613800-38635600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:38613800-38636600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:38613800-38639000	Weak transcription	Left Ventricle	heart
20	chr19:38613800-38641800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:38613800-38643200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:38614000-38634800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr19:38616200-38641600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr19:38616600-38642000	Weak transcription	Dnd41	blood
28	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
29	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
30	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
31	chr19:38621000-38633800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr19:38621600-38642800	Weak transcription	NHLF	lung
33	chr19:38621800-38634000	Weak transcription	Thymus	Thymus
34	chr19:38622000-38634600	Weak transcription	Brain Germinal Matrix	brain
35	chr19:38622200-38636800	Weak transcription	Brain Anterior Caudate	brain
36	chr19:38622400-38634000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:38622600-38641800	Weak transcription	Aorta	Aorta
38	chr19:38622800-38634000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:38622800-38634600	Weak transcription	Adipose Nuclei	Adipose
40	chr19:38622800-38634800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:38623000-38635200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:38623000-38642800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr19:38623200-38634400	Weak transcription	Fetal Brain Female	brain
44	chr19:38624000-38633200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:38624400-38652400	Weak transcription	Fetal Thymus	thymus
46	chr19:38624600-38633400	Weak transcription	Fetal Lung	lung
47	chr19:38624800-38633200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:38626000-38643400	Weak transcription	Placenta	Placenta
49	chr19:38626200-38634600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:38626400-38633400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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