Variant report

Variant	rs12534969
Chromosome Location	chr7:101669053-101669054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:101663065..101665225-chr7:101668023..101670728,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10231704	0.94[LWK][hapmap]
rs10245459	0.84[LWK][hapmap]
rs10249739	0.84[LWK][hapmap]
rs10252737	0.84[LWK][hapmap]
rs10259603	1.00[CHD][hapmap]
rs10274188	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10488042	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10488043	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs12537526	1.00[CHD][hapmap]
rs12668959	1.00[CHD][hapmap]
rs12672026	1.00[CHD][hapmap]
rs17494372	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202147	1.00[CHD][hapmap]
rs2158902	0.92[ASN][1000 genomes]
rs28461243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973312	1.00[CHD][hapmap]
rs73185860	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405966	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7780631	1.00[CHD][hapmap]
rs7797764	1.00[CHD][hapmap]
rs7799663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805379	1.00[CHD][hapmap]

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	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1027574	chr7:101654060-101718950	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12534969	DPY19L2P2	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101578200-101671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:101627000-101671200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:101641600-101672000	Weak transcription	K562	blood
4	chr7:101642200-101671400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:101642200-101671600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:101642200-101674600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:101642400-101671200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:101642400-101671400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:101642400-101675400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:101642800-101697600	Weak transcription	Primary B cells from cord blood	blood
11	chr7:101643000-101672800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:101643000-101675600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:101646800-101671600	Weak transcription	GM12878-XiMat	blood
14	chr7:101648200-101671200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:101648200-101681400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:101648200-101688000	Weak transcription	Ovary	ovary
17	chr7:101649000-101671400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:101649400-101672800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:101649800-101671600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:101652400-101671600	Weak transcription	Pancreas	Pancrea
21	chr7:101652400-101683200	Weak transcription	Right Ventricle	heart
22	chr7:101652800-101688400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:101653000-101671400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:101653000-101688200	Weak transcription	Colonic Mucosa	Colon
25	chr7:101653200-101685200	Weak transcription	HSMMtube	muscle
26	chr7:101653400-101671600	Weak transcription	Gastric	stomach
27	chr7:101653600-101671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:101654200-101671400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:101655800-101671400	Weak transcription	Adipose Nuclei	Adipose
30	chr7:101656000-101682800	Weak transcription	Psoas Muscle	Psoas
31	chr7:101656000-101689200	Weak transcription	Aorta	Aorta
32	chr7:101656200-101671400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:101656800-101681400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:101657000-101672000	Weak transcription	Fetal Lung	lung
35	chr7:101657000-101681400	Weak transcription	Osteobl	bone
36	chr7:101657200-101671600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr7:101657200-101677000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:101657800-101671400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:101662400-101671800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:101662800-101671200	Weak transcription	Spleen	Spleen
41	chr7:101664600-101676400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr7:101665600-101671400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr7:101665600-101688000	Weak transcription	Brain Angular Gyrus	brain
44	chr7:101665800-101671200	Weak transcription	Fetal Stomach	stomach
45	chr7:101665800-101671400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr7:101665800-101671600	Weak transcription	Lung	lung
47	chr7:101666000-101669200	Enhancers	Thymus	Thymus
48	chr7:101666000-101671600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:101666200-101671600	Weak transcription	NHEK	skin
50	chr7:101666400-101671400	Enhancers	Fetal Thymus	thymus

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