Variant report

Variant	rs8108762
Chromosome Location	chr19:45653227-45653228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45652567..45654233-chr19:45681921..45683559,2	MCF-7	breast:
2	chr19:45640475..45642060-chr19:45652557..45654572,2	MCF-7	breast:
3	chr19:45648191..45651318-chr19:45652739..45655136,4	MCF-7	breast:
4	chr19:45651718..45653898-chr19:45656029..45658572,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKPD1-2	chr19:45653008-45653863	ENSG00000267037.1

Variant related genes	Relation type
ENSG00000104866	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000179846	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11666681	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11672002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672271	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12975698	0.81[CEU][hapmap]
rs12977416	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12981729	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12984180	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3178166	0.83[ASN][1000 genomes]
rs35620552	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35836101	0.81[EUR][1000 genomes]
rs3745157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62118469	0.80[ASN][1000 genomes]
rs62118470	0.80[ASN][1000 genomes]
rs7251736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255018	0.80[EUR][1000 genomes]
rs8109620	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs968445	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv522341	chr19:45640124-45664218	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8108762	GEMIN7	cis	cerebellar cortex	BrainEAC

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45625000-45654200	Weak transcription	NHDF-Ad	bronchial
2	chr19:45626200-45653400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:45627600-45655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:45633600-45655200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:45639800-45656800	Weak transcription	K562	blood
6	chr19:45640000-45653800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:45640000-45654400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:45640400-45655000	Weak transcription	Fetal Heart	heart
9	chr19:45641400-45654600	Weak transcription	HSMM	muscle
10	chr19:45641600-45654000	Weak transcription	HSMMtube	muscle
11	chr19:45641800-45653800	Weak transcription	Stomach Mucosa	stomach
12	chr19:45642000-45653600	Strong transcription	Fetal Intestine Small	intestine
13	chr19:45642000-45655200	Weak transcription	GM12878-XiMat	blood
14	chr19:45642000-45655400	Weak transcription	Right Atrium	heart
15	chr19:45642800-45653400	Strong transcription	Fetal Stomach	stomach
16	chr19:45643000-45654200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:45643000-45654200	Strong transcription	Gastric	stomach
18	chr19:45643400-45653600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:45643600-45654000	Weak transcription	HMEC	breast
20	chr19:45643800-45653400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:45644600-45653800	Weak transcription	HepG2	liver
22	chr19:45646000-45655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:45646600-45654000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:45646600-45655000	Weak transcription	Primary B cells from cord blood	blood
25	chr19:45646800-45655000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:45647000-45654400	Weak transcription	Brain Substantia Nigra	brain
27	chr19:45647000-45654600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:45647000-45655400	Weak transcription	Left Ventricle	heart
29	chr19:45647200-45654200	Weak transcription	Fetal Lung	lung
30	chr19:45648600-45654800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:45649000-45653600	Weak transcription	Psoas Muscle	Psoas
32	chr19:45649600-45654200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:45649800-45654400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:45649800-45654800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:45650000-45654200	Weak transcription	NHEK	skin
36	chr19:45650000-45655200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:45650000-45655400	Weak transcription	Liver	Liver
38	chr19:45650000-45655800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:45650200-45653400	Weak transcription	Adipose Nuclei	Adipose
40	chr19:45650200-45653800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:45650200-45653800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr19:45650200-45654400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:45650200-45654400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr19:45650200-45654800	Weak transcription	Osteobl	bone
45	chr19:45650200-45655200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:45650200-45655600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:45650400-45654000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:45650400-45654200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr19:45650600-45653800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:45650600-45654200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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