Variant report

Variant	rs12594938
Chromosome Location	chr15:73071282-73071283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73070867..73073438-chr15:73080121..73082937,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11072384	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11072387	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439375	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12440951	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12594667	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12594844	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16957293	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2012253	0.82[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2278543	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2415166	0.91[ASN][1000 genomes]
rs28398258	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3179616	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35136341	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3759870	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3850988	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4776611	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4776616	0.91[ASN][1000 genomes]
rs4777528	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4777529	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs4777530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4777531	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4777533	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4777537	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4777538	0.97[ASN][1000 genomes]
rs4777540	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4777543	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4777545	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56915357	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57621041	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58600393	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59049627	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60601886	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60674997	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61311866	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62017593	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62017598	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62017623	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7178409	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs72662112	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72737337	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs730180	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7495022	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7497429	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8032586	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8033644	0.82[CHB][hapmap];0.84[MEX][hapmap]

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	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv482512	chr15:73023099-73175952	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12594938	BBS4	cis	brain	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73043800-73073600	Strong transcription	Fetal Thymus	thymus
2	chr15:73045000-73074200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:73045200-73074200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:73048600-73075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:73060000-73074000	Weak transcription	Stomach Mucosa	stomach
6	chr15:73060000-73075000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:73060200-73075200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:73060400-73073200	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:73060600-73072000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:73061400-73073400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:73061400-73073600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:73061400-73075000	Weak transcription	Fetal Kidney	kidney
13	chr15:73062600-73073600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:73062800-73073800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:73062800-73074000	Weak transcription	Small Intestine	intestine
16	chr15:73064000-73071400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:73065000-73072800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:73065000-73073800	Weak transcription	HMEC	breast
19	chr15:73065000-73074200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:73065200-73073800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:73065400-73074000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:73065400-73074200	Weak transcription	Brain Germinal Matrix	brain
23	chr15:73065600-73073600	Weak transcription	Brain Anterior Caudate	brain
24	chr15:73065800-73073200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:73066000-73073600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:73066400-73073800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:73066800-73072800	Weak transcription	Fetal Lung	lung
28	chr15:73066800-73074200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:73067000-73073200	Weak transcription	Spleen	Spleen
30	chr15:73067000-73074200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:73067000-73075000	Weak transcription	Esophagus	oesophagus
32	chr15:73067200-73073200	Weak transcription	Gastric	stomach
33	chr15:73067200-73073400	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:73067200-73073600	Weak transcription	Brain Substantia Nigra	brain
35	chr15:73067200-73074000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:73067400-73072000	Weak transcription	Osteobl	bone
37	chr15:73067400-73072600	Weak transcription	Fetal Intestine Small	intestine
38	chr15:73067400-73072800	Weak transcription	Pancreas	Pancrea
39	chr15:73067400-73073200	Weak transcription	Thymus	Thymus
40	chr15:73067400-73073400	Weak transcription	Brain Angular Gyrus	brain
41	chr15:73067400-73073600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:73067400-73073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:73067400-73073600	Weak transcription	NHLF	lung
44	chr15:73067400-73073800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:73067400-73073800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr15:73067400-73074000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:73067400-73074000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr15:73067400-73074200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:73067400-73074200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:73067400-73074200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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