Variant report

Variant	rs11672271
Chromosome Location	chr19:45619946-45619947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45614303..45618965-chr19:45619228..45622804,6	K562	blood:
2	chr19:45609578..45611923-chr19:45617060..45620020,2	K562	blood:
3	chr19:45573175..45575144-chr19:45618642..45620266,2	MCF-7	breast:
4	chr19:45577654..45580271-chr19:45618383..45621164,2	MCF-7	breast:
5	chr19:45619288..45621355-chr19:45634248..45636260,2	MCF-7	breast:
6	chr19:45606192..45609291-chr19:45618096..45620954,3	K562	blood:

Variant related genes	Relation type
ENSG00000170684	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11666681	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11672002	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];0.85[CHB][hapmap]
rs12977416	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12981729	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12984180	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35620552	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35836101	0.84[EUR][1000 genomes]
rs3745157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7255018	0.83[EUR][1000 genomes]
rs8108762	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8109620	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs968445	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11672271	GEMIN7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45606600-45623400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:45606600-45624800	Weak transcription	NHEK	skin
3	chr19:45606800-45621000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:45606800-45634000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr19:45607200-45625600	Weak transcription	NHLF	lung
6	chr19:45607600-45626600	Weak transcription	Fetal Brain Male	brain
7	chr19:45607800-45620400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:45607800-45620600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:45608000-45620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr19:45608000-45639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:45608400-45629200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:45608600-45621000	Weak transcription	Fetal Brain Female	brain
13	chr19:45609000-45621400	Weak transcription	Right Atrium	heart
14	chr19:45609200-45620600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:45609200-45620600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:45610400-45644400	Weak transcription	Aorta	Aorta
17	chr19:45613200-45623600	Weak transcription	Ovary	ovary
18	chr19:45613400-45621800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:45614200-45623000	Enhancers	Stomach Mucosa	stomach
20	chr19:45615600-45620200	Enhancers	Lung	lung
21	chr19:45615600-45629800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:45615800-45620600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr19:45616000-45622000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:45616000-45623200	Enhancers	Pancreas	Pancrea
25	chr19:45616200-45621000	Weak transcription	Small Intestine	intestine
26	chr19:45616400-45620600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:45616400-45623400	Enhancers	Fetal Muscle Leg	muscle
28	chr19:45616800-45620800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:45617000-45620600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr19:45617000-45625400	Enhancers	Fetal Muscle Trunk	muscle
31	chr19:45617000-45651600	Weak transcription	Fetal Kidney	kidney
32	chr19:45617200-45622000	Enhancers	Fetal Intestine Large	intestine
33	chr19:45617200-45627800	Enhancers	Fetal Thymus	thymus
34	chr19:45617400-45620000	Strong transcription	Fetal Stomach	stomach
35	chr19:45617400-45620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:45617400-45620600	Weak transcription	Placenta	Placenta
37	chr19:45617400-45620600	Weak transcription	HMEC	breast
38	chr19:45617400-45621600	Enhancers	Duodenum Mucosa	Duodenum
39	chr19:45617400-45633200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:45617600-45620600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:45617600-45620600	Weak transcription	HepG2	liver
42	chr19:45617600-45620800	Weak transcription	Liver	Liver
43	chr19:45617800-45620600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:45617800-45620600	Weak transcription	A549	lung
45	chr19:45617800-45640000	Weak transcription	Fetal Lung	lung
46	chr19:45618400-45621400	Enhancers	Dnd41	blood
47	chr19:45618400-45622200	Enhancers	Right Ventricle	heart
48	chr19:45618600-45620600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr19:45618600-45620600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr19:45618600-45620600	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links