Variant report

Variant	rs7957659
Chromosome Location	chr12:50638810-50638811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50633929..50638139-chr12:50638624..50643008,10	K562	blood:
2	chr12:50612347..50619665-chr12:50638648..50642431,12	K562	blood:
3	chr12:50612347..50617844-chr12:50638648..50642831,7	K562	blood:
4	chr12:50637253..50639718-chr12:50676193..50678822,2	MCF-7	breast:
5	chr12:50637092..50639387-chr12:50653730..50656113,2	K562	blood:

Variant related genes	Relation type
ENSG00000050405	Chromatin interaction
ENSG00000203433	Chromatin interaction
ENSG00000257256	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10219559	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1044370	0.81[ASW][hapmap]
rs10747573	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10783342	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783343	0.91[AMR][1000 genomes]
rs1362984	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1862042	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2004283	0.91[AMR][1000 genomes]
rs2160994	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs2178173	0.88[YRI][hapmap]
rs2358538	1.00[ASW][hapmap];0.97[GIH][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap]
rs4459386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580729	0.81[ASW][hapmap]
rs6580732	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580734	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580736	0.87[LWK][hapmap]
rs7136570	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7136648	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7279	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7297421	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7301566	0.85[EUR][1000 genomes]
rs7302981	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7308692	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7309519	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532	0.89[ASW][hapmap]
rs7967954	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181679	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9668955	0.88[AMR][1000 genomes];0.82[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
5	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7957659	LASS5	cis	parietal	SCAN
rs7957659	NELL2	cis	cerebellum	SCAN
rs7957659	CERS5	cis	Nerve Tibial	GTEx
rs7957659	MCRS1	cis	parietal	SCAN
rs7957659	DIP2B	cis	cerebellum	SCAN
rs7957659	LASS5	cis	multi-tissue	Pritchard
rs7957659	LASS5	cis	cerebellum	SCAN
rs7957659	SMARCD1	cis	cerebellum	SCAN
rs7957659	SLC4A8	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50616800-50641600	Weak transcription	Brain Angular Gyrus	brain
2	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
3	chr12:50618600-50640000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:50627600-50644600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:50628800-50640800	Weak transcription	Esophagus	oesophagus
6	chr12:50633200-50651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:50633600-50643400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:50634000-50640200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:50634200-50641000	Weak transcription	Lung	lung
10	chr12:50634200-50643400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:50634600-50648200	Weak transcription	Spleen	Spleen
12	chr12:50634800-50640400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:50635600-50640000	Weak transcription	Psoas Muscle	Psoas
14	chr12:50635600-50640200	Weak transcription	Liver	Liver
15	chr12:50635600-50642400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:50635600-50646600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:50636000-50643000	Genic enhancers	Fetal Intestine Large	intestine
18	chr12:50636200-50639000	Genic enhancers	Fetal Intestine Small	intestine
19	chr12:50636200-50651200	Weak transcription	Fetal Kidney	kidney
20	chr12:50636400-50640800	Weak transcription	Pancreas	Pancrea
21	chr12:50636400-50641200	Weak transcription	Right Ventricle	heart
22	chr12:50636600-50639400	Enhancers	Adipose Nuclei	Adipose
23	chr12:50636600-50639400	Weak transcription	Left Ventricle	heart
24	chr12:50636600-50640400	Weak transcription	Fetal Thymus	thymus
25	chr12:50636600-50640400	Weak transcription	Right Atrium	heart
26	chr12:50636600-50640800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:50636600-50640800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr12:50636600-50642400	Weak transcription	Ovary	ovary
29	chr12:50636600-50651400	Weak transcription	Gastric	stomach
30	chr12:50636600-50651800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:50636800-50640400	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:50636800-50641200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:50636800-50642000	Weak transcription	Small Intestine	intestine
34	chr12:50636800-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:50637200-50639400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:50637200-50640000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:50637200-50640200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:50637200-50640800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:50637200-50641400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:50637200-50641600	Enhancers	NHDF-Ad	bronchial
41	chr12:50637200-50645600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:50637200-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:50637400-50639600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:50637400-50640200	Weak transcription	Aorta	Aorta
45	chr12:50637400-50640400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:50637400-50643400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:50637600-50639400	Weak transcription	NHEK	skin
48	chr12:50637600-50639600	Weak transcription	HMEC	breast
49	chr12:50637600-50640000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:50637600-50640000	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links