Variant report

Variant	rs2356751
Chromosome Location	chr19:44649590-44649591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44644894..44647318-chr19:44647598..44649743,2	MCF-7	breast:
2	chr19:44644376..44645902-chr19:44648536..44650255,2	MCF-7	breast:
3	chr19:44648468..44650180-chr19:44664736..44666479,2	K562	blood:
4	chr19:44619756..44622526-chr19:44648791..44651550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263002	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10405450	0.89[ASN][1000 genomes]
rs10409155	0.90[EUR][1000 genomes]
rs10410086	0.89[ASN][1000 genomes]
rs10423306	0.83[ASN][1000 genomes]
rs10425945	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs11667521	0.81[GIH][hapmap]
rs12460039	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12462557	0.83[GIH][hapmap]
rs12462723	0.83[GIH][hapmap]
rs12608984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2085516	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2100643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2168989	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs2232801	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs2279072	0.81[GIH][hapmap];0.81[YRI][hapmap]
rs2279073	0.81[GIH][hapmap]
rs2293587	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356752	0.88[EUR][1000 genomes]
rs3817595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802209	0.90[EUR][1000 genomes]
rs4802210	0.87[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4803684	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs56357907	0.92[ASN][1000 genomes]
rs58778698	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60668498	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61412562	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61589395	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62117770	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6509146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7248114	0.91[ASN][1000 genomes]
rs7249209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251682	0.81[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs7253533	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs7260304	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs8103838	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs9304640	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9646643	0.80[GIH][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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2356751	ZNF575	cis	lymphoblastoid	seeQTL
rs2356751	SIGLEC9	cis	parietal	SCAN
rs2356751	APOC1	cis	parietal	SCAN
rs2356751	DHDH	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44646600-44649600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:44646600-44650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:44646600-44652800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:44646600-44653400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:44646800-44649600	Weak transcription	Fetal Stomach	stomach
6	chr19:44646800-44651400	Weak transcription	Fetal Intestine Small	intestine
7	chr19:44646800-44651400	Weak transcription	Pancreas	Pancrea
8	chr19:44646800-44651600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:44646800-44652200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:44646800-44652200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:44646800-44652200	Weak transcription	Small Intestine	intestine
12	chr19:44646800-44652800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:44646800-44653800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:44646800-44656600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:44646800-44657800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:44646800-44660200	Weak transcription	Stomach Mucosa	stomach
17	chr19:44647000-44649800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:44647000-44650000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:44647000-44650200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:44647000-44650200	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:44647000-44650200	Weak transcription	HepG2	liver
22	chr19:44647000-44652000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:44647000-44652200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:44647000-44652200	Weak transcription	Brain Angular Gyrus	brain
25	chr19:44647000-44652200	Weak transcription	Fetal Kidney	kidney
26	chr19:44647000-44652200	Weak transcription	Fetal Lung	lung
27	chr19:44647000-44652400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:44647000-44652400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:44647000-44654200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:44647000-44655600	Weak transcription	HUVEC	blood vessel
31	chr19:44647000-44660200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:44647000-44660200	Weak transcription	Hela-S3	cervix
33	chr19:44647000-44660400	Weak transcription	Fetal Heart	heart
34	chr19:44647400-44652400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:44647600-44655800	Weak transcription	Fetal Brain Male	brain
36	chr19:44647800-44668400	ZNF genes & repeats	Liver	Liver
37	chr19:44648000-44650800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:44648200-44650400	Strong transcription	Brain Hippocampus Middle	brain
39	chr19:44648200-44650400	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr19:44648200-44650800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:44648200-44651000	Strong transcription	Osteobl	bone
42	chr19:44648200-44652200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr19:44648200-44652400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr19:44648200-44656400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr19:44648200-44657600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:44648200-44658200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:44648200-44660000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:44648400-44649800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr19:44648400-44650200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:44648400-44650200	Strong transcription	HSMM	muscle

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