Variant report

Variant	rs7301943
Chromosome Location	chr12:29720014-29720015
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	chr12:29713988..29716071-chr12:29717724..29720269,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10492311	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11050323	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs11829731	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11829994	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11834102	0.91[EUR][1000 genomes]
rs11834291	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11837554	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs12310251	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12424239	0.85[EUR][1000 genomes]
rs12822100	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12826893	0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs12826911	0.89[CHB][hapmap]
rs12828728	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs142565	0.91[CEU][hapmap];0.89[CHB][hapmap];0.96[EUR][1000 genomes]
rs148897	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159684	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs159688	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs159691	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs159692	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs159693	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16934418	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs16934448	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16934474	0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16934523	1.00[CHB][hapmap]
rs16934537	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs16934556	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16934564	1.00[CHB][hapmap]
rs16934569	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16934597	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16934635	0.89[CHB][hapmap]
rs2288228	0.81[CEU][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs299474	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs299477	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[TSI][hapmap]
rs299478	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs299480	0.96[EUR][1000 genomes]
rs299482	1.00[CHB][hapmap]
rs299483	1.00[CHB][hapmap]
rs299484	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs299485	0.91[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs34318689	0.85[EUR][1000 genomes]
rs55793838	0.91[AMR][1000 genomes]
rs55970961	0.91[AMR][1000 genomes]
rs56178040	0.81[ASN][1000 genomes]
rs56255721	0.91[AMR][1000 genomes]
rs56367916	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56398900	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57816450	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58290227	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59519970	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59915017	0.91[AMR][1000 genomes]
rs67491988	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73069592	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73069593	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73069598	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73071505	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73071510	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73071517	0.88[EUR][1000 genomes]
rs73071519	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73071533	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73071556	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73071582	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7315541	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74078415	0.94[AMR][1000 genomes];0.88[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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7301943	SYT10	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
3	chr12:29709800-29756200	Weak transcription	HMEC	breast
4	chr12:29711800-29720800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:29712600-29722200	Weak transcription	Colonic Mucosa	Colon
6	chr12:29712600-29734600	Weak transcription	Liver	Liver
7	chr12:29712800-29722200	Weak transcription	Brain Germinal Matrix	brain
8	chr12:29713200-29726400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:29713200-29726600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:29713200-29731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:29715400-29721400	Weak transcription	Esophagus	oesophagus
13	chr12:29715400-29722200	Weak transcription	Fetal Lung	lung
14	chr12:29715400-29731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:29715800-29724800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:29716400-29721000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:29716400-29722200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:29717000-29721800	Weak transcription	HUVEC	blood vessel
20	chr12:29717400-29720400	Weak transcription	Fetal Heart	heart
21	chr12:29717400-29722200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:29717600-29721600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:29717600-29721600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:29717600-29725000	Weak transcription	Aorta	Aorta
25	chr12:29717600-29727400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:29717600-29727800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:29717600-29734800	Weak transcription	NHLF	lung
28	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
29	chr12:29717800-29721600	Weak transcription	HSMMtube	muscle
30	chr12:29717800-29732200	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:29718000-29720200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:29718200-29725400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:29718600-29727600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:29718800-29720200	Enhancers	Ovary	ovary
35	chr12:29718800-29723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:29719000-29720200	Enhancers	Gastric	stomach
37	chr12:29719200-29720200	Enhancers	Adipose Nuclei	Adipose
38	chr12:29719200-29721800	Weak transcription	HSMM	muscle
39	chr12:29719400-29720200	Enhancers	Fetal Muscle Trunk	muscle
40	chr12:29719400-29720200	Enhancers	Osteobl	bone
41	chr12:29719400-29721400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:29719400-29722800	Enhancers	Fetal Kidney	kidney
43	chr12:29719400-29724000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:29719600-29720200	Enhancers	Fetal Muscle Leg	muscle
45	chr12:29719600-29720200	Enhancers	NHDF-Ad	bronchial
46	chr12:29719600-29720600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr12:29719600-29721800	Weak transcription	NH-A	brain
48	chr12:29719600-29722200	Weak transcription	Fetal Stomach	stomach
49	chr12:29719600-29724600	Weak transcription	Right Ventricle	heart
50	chr12:29719600-29724600	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links