Variant report

Variant	rs7953537
Chromosome Location	chr12:44693288-44693289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10506243	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10506244	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506245	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11182470	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11182477	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12300292	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1527315	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17094382	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17094386	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17094396	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17094401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17094405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17094408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17094412	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17094421	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17094423	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17094437	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17094458	1.00[EUR][1000 genomes]
rs17094465	0.92[EUR][1000 genomes]
rs17094473	0.92[EUR][1000 genomes]
rs17094505	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17094509	0.92[EUR][1000 genomes]
rs17094532	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17094560	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17094577	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1716605	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1726889	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1948424	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2080876	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3858725	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4307772	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4544066	0.92[EUR][1000 genomes]
rs4573751	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7296406	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73276261	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74084494	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7966220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975491	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7979252	1.00[MEX][hapmap]
rs840774	1.00[CEU][hapmap];0.92[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	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv686	chr12:44671240-44696910	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	n/a
3	nsv1038498	chr12:44679455-44816572	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2599381	chr12:44691231-44693475	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7953537	MDK	trans	brain	seeQTL
rs7953537	HSPA6	trans	brain	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44676600-44697800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:44682000-44698600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:44685000-44695400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:44688800-44702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:44690400-44697800	Weak transcription	HSMMtube	muscle
6	chr12:44690400-44698000	Weak transcription	Liver	Liver
7	chr12:44690400-44698600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:44690600-44697800	Weak transcription	Aorta	Aorta
9	chr12:44690600-44697800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:44690800-44694800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:44690800-44696000	Weak transcription	Pancreas	Pancrea
12	chr12:44690800-44698000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:44690800-44698000	Weak transcription	Esophagus	oesophagus
14	chr12:44690800-44701400	Weak transcription	Left Ventricle	heart
15	chr12:44691400-44701400	Weak transcription	Psoas Muscle	Psoas
16	chr12:44692600-44693600	Weak transcription	Fetal Intestine Large	intestine
17	chr12:44693000-44693400	Weak transcription	Fetal Intestine Small	intestine
18	chr12:44693200-44693600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:44693200-44693600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:44693200-44693600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:44693200-44694200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr12:44693200-44694200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr12:44693200-44694200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:44693200-44694200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr12:44693200-44694200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr12:44693200-44694400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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