Variant report

Variant	rs11672002
Chromosome Location	chr19:45624987-45624988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45576178..45580996-chr19:45624559..45629632,6	MCF-7	breast:
2	chr19:45577914..45580409-chr19:45622288..45626945,5	MCF-7	breast:
3	chr19:45624743..45627700-chr19:45634082..45635925,2	K562	blood:
4	chr19:45617752..45619643-chr19:45623341..45625344,2	K562	blood:
5	chr19:45602073..45604074-chr19:45623767..45626088,2	K562	blood:

Variant related genes	Relation type
ENSG00000104866	Chromatin interaction
ENSG00000170684	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11666681	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11672271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12975698	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12977416	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12981729	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984180	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3178166	0.87[ASN][1000 genomes]
rs35620552	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35836101	0.83[EUR][1000 genomes]
rs3745157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62118469	0.84[ASN][1000 genomes]
rs62118470	0.84[ASN][1000 genomes]
rs7251736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255018	0.82[EUR][1000 genomes]
rs8108762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8109620	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.84[ASN][1000 genomes]
rs968445	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449420	chr19:45523560-45626884	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11672002	BIRC8	cis	parietal	SCAN
rs11672002	GRLF1	cis	parietal	SCAN
rs11672002	CPT1C	cis	parietal	SCAN
rs11672002	LIN7B	cis	cerebellum	SCAN
rs11672002	TBC1D17	cis	parietal	SCAN
rs11672002	VN1R4	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45606800-45634000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr19:45607200-45625600	Weak transcription	NHLF	lung
3	chr19:45607600-45626600	Weak transcription	Fetal Brain Male	brain
4	chr19:45608000-45639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:45608400-45629200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:45610400-45644400	Weak transcription	Aorta	Aorta
7	chr19:45615600-45629800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:45617000-45625400	Enhancers	Fetal Muscle Trunk	muscle
9	chr19:45617000-45651600	Weak transcription	Fetal Kidney	kidney
10	chr19:45617200-45627800	Enhancers	Fetal Thymus	thymus
11	chr19:45617400-45633200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:45617800-45640000	Weak transcription	Fetal Lung	lung
13	chr19:45618600-45625800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:45618800-45639600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:45618800-45639600	Weak transcription	Brain Substantia Nigra	brain
16	chr19:45619200-45625800	Enhancers	Primary B cells from peripheral blood	blood
17	chr19:45619400-45625600	Enhancers	Primary B cells from cord blood	blood
18	chr19:45619800-45626200	Enhancers	Primary hematopoietic stem cells	blood
19	chr19:45620000-45633400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:45620600-45627800	Genic enhancers	Fetal Intestine Small	intestine
21	chr19:45620800-45643800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:45621000-45629400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:45621000-45634000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:45621000-45634000	Weak transcription	HSMMtube	muscle
25	chr19:45621200-45625200	Weak transcription	HMEC	breast
26	chr19:45621200-45629200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr19:45621200-45629600	Weak transcription	HepG2	liver
28	chr19:45621200-45633800	Weak transcription	Osteobl	bone
29	chr19:45621200-45639800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:45621200-45644000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr19:45621400-45625200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:45621400-45629200	Weak transcription	A549	lung
33	chr19:45621400-45633400	Weak transcription	Dnd41	blood
34	chr19:45621400-45635000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr19:45621600-45629200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:45621600-45629200	Weak transcription	Brain Anterior Caudate	brain
37	chr19:45621600-45643800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:45621800-45629200	Weak transcription	Small Intestine	intestine
39	chr19:45621800-45639800	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:45622000-45625400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:45622000-45629000	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:45622000-45629000	Weak transcription	K562	blood
43	chr19:45622000-45639200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:45622200-45625000	Weak transcription	Right Ventricle	heart
45	chr19:45622200-45625000	Enhancers	GM12878-XiMat	blood
46	chr19:45622200-45625400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:45622200-45626600	Weak transcription	Adipose Nuclei	Adipose
48	chr19:45622200-45629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:45622200-45629200	Weak transcription	Brain Angular Gyrus	brain
50	chr19:45622200-45629200	Weak transcription	Right Atrium	heart

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