Variant report

Variant	rs7975492
Chromosome Location	chr12:122827668-122827669
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122805766..122808468-chr12:122824951..122827669,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10161184	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10161488	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10773090	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773108	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10773117	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846714	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846852	0.82[EUR][1000 genomes]
rs10846912	0.81[CEU][hapmap];0.94[CHB][hapmap]
rs11057514	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11057522	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057686	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057813	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057819	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1129167	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11503023	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12812332	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs12818177	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12828876	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12829449	0.83[EUR][1000 genomes]
rs1392142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1532579	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1553178	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2341438	0.82[EUR][1000 genomes]
rs3825096	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs4758664	0.81[EUR][1000 genomes]
rs4758665	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758692	0.81[GIH][hapmap]
rs4758693	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758695	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs61021925	0.83[EUR][1000 genomes]
rs6488947	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305360	0.81[EUR][1000 genomes]
rs7313121	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7313284	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959550	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7961258	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7970007	0.81[EUR][1000 genomes]
rs7972832	0.84[EUR][1000 genomes]
rs7973480	0.84[EUR][1000 genomes]
rs7974160	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978119	0.81[EUR][1000 genomes]
rs7978636	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868181	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788228	0.95[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7975492	NME2P1	cis	parietal	SCAN
rs7975492	CCDC62	cis	cerebellum	SCAN
rs7975492	NME2P1	cis	cerebellum	SCAN
rs7975492	DYNLL1	cis	parietal	SCAN
rs7975492	GATC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122775600-122833600	Strong transcription	Liver	Liver
2	chr12:122791200-122841600	Strong transcription	Placenta	Placenta
3	chr12:122794600-122832600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:122804200-122839000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:122812800-122829400	Weak transcription	Fetal Heart	heart
6	chr12:122812800-122839400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:122812800-122839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:122812800-122844000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:122812800-122850600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:122813000-122839400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:122818200-122838200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:122818400-122831000	Weak transcription	Pancreas	Pancrea
13	chr12:122818400-122852800	Weak transcription	Stomach Mucosa	stomach
14	chr12:122818600-122837000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:122818600-122844200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:122819600-122831400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:122819600-122835200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:122819600-122835800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:122819600-122837000	Weak transcription	Thymus	Thymus
20	chr12:122819600-122839200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:122819800-122831600	Weak transcription	Fetal Brain Male	brain
22	chr12:122819800-122835600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:122819800-122837000	Weak transcription	Colonic Mucosa	Colon
24	chr12:122819800-122837400	Weak transcription	Small Intestine	intestine
25	chr12:122820000-122830600	Weak transcription	Brain Substantia Nigra	brain
26	chr12:122820000-122831000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:122820000-122831200	Weak transcription	Gastric	stomach
28	chr12:122820000-122835400	Weak transcription	Dnd41	blood
29	chr12:122820200-122833400	Weak transcription	HepG2	liver
30	chr12:122820200-122835000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:122820200-122839400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:122820600-122831000	Weak transcription	Esophagus	oesophagus
33	chr12:122820600-122831200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:122821400-122835400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:122821800-122831800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:122822000-122829600	Weak transcription	Fetal Intestine Small	intestine
37	chr12:122822400-122837000	Weak transcription	GM12878-XiMat	blood
38	chr12:122822600-122828400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:122823000-122840200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:122823200-122828600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:122823200-122828600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:122823200-122829800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:122823200-122839400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:122823800-122829800	Strong transcription	HSMM	muscle
45	chr12:122823800-122834200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:122824000-122834400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:122824200-122829400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:122824400-122833600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:122824600-122830800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:122825000-122828600	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links