Variant report

Variant	rs12173582
Chromosome Location	chr6:35340300-35340301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35339706..35342371-chr6:35345441..35347439,2	K562	blood:
2	chr6:35330201..35332788-chr6:35338848..35341376,3	K562	blood:
3	chr6:35335380..35337947-chr6:35338128..35341057,2	MCF-7	breast:
4	chr6:35329439..35333357-chr6:35335770..35342563,9	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10080361	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10080411	0.84[ASN][1000 genomes]
rs10755687	0.86[CHD][hapmap]
rs10807150	0.87[CHD][hapmap]
rs10947540	0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1194	0.94[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12173347	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211765	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12211943	0.81[ASN][1000 genomes]
rs13214290	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs1557567	0.86[CHD][hapmap]
rs1557568	0.87[CHD][hapmap]
rs1888822	0.85[JPT][hapmap]
rs1888823	0.94[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1888824	0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1888825	0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1894650	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1894651	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1894652	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1894653	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1929847	0.94[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1929849	0.94[CHD][hapmap];0.95[JPT][hapmap]
rs1987673	0.87[CHD][hapmap]
rs2032538	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs2071920	0.87[CHD][hapmap]
rs2183834	0.85[ASN][1000 genomes]
rs2267657	0.87[CHD][hapmap]
rs2267660	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267661	0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267662	0.94[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2267663	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2267664	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2284195	0.81[ASN][1000 genomes]
rs2284196	0.83[ASN][1000 genomes]
rs2395621	0.82[ASN][1000 genomes]
rs3777744	0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs3798342	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798343	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800382	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3800383	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3800385	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs3800386	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3800387	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3800388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3800392	0.95[JPT][hapmap]
rs3800400	0.89[EUR][1000 genomes]
rs4583983	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711411	0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4711413	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711414	0.81[ASN][1000 genomes]
rs4713845	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4713848	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713850	0.81[ASN][1000 genomes]
rs4713853	0.80[ASN][1000 genomes]
rs58925593	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62403575	0.81[ASN][1000 genomes]
rs6902523	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6907324	0.81[ASN][1000 genomes]
rs6907573	0.85[ASN][1000 genomes]
rs6913037	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6920747	0.81[ASN][1000 genomes]
rs6938946	0.94[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7769906	0.81[ASN][1000 genomes]
rs7772212	0.81[ASN][1000 genomes]
rs914547	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs9296144	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9296150	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348974	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366883	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9366885	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368852	0.89[EUR][1000 genomes]
rs9368853	0.89[EUR][1000 genomes]
rs9368854	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9368857	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368859	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368860	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368865	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380500	0.95[JPT][hapmap]
rs9380501	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380502	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380505	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380507	1.00[EUR][1000 genomes]
rs9394288	0.95[JPT][hapmap]
rs9394289	0.81[ASN][1000 genomes]
rs9462072	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9469964	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs9469972	0.87[CHD][hapmap]
rs9469979	0.80[ASN][1000 genomes]
rs9469997	0.81[ASN][1000 genomes]
rs975496	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs991145	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12173582	SCGB1D2	trans	brain	seeQTL
rs12173582	SCGB2A2	trans	brain	seeQTL
rs12173582	GREM1	trans	brain	seeQTL
rs12173582	TFF1	trans	brain	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35321000-35342400	Weak transcription	Fetal Kidney	kidney
2	chr6:35328400-35344800	Weak transcription	Fetal Lung	lung
3	chr6:35329000-35350800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:35331200-35350800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:35331600-35345400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:35331600-35345400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:35335800-35340400	Enhancers	Spleen	Spleen
8	chr6:35337200-35341400	Enhancers	Brain Hippocampus Middle	brain
9	chr6:35337800-35340800	Enhancers	Liver	Liver
10	chr6:35338200-35344400	Weak transcription	Aorta	Aorta
11	chr6:35338200-35344800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:35338200-35356400	Weak transcription	Pancreas	Pancrea
13	chr6:35338400-35350800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:35338400-35378400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:35338600-35344200	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:35338600-35345400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:35338600-35359400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:35338800-35340600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr6:35338800-35341000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr6:35338800-35342800	Weak transcription	Thymus	Thymus
21	chr6:35338800-35344800	Weak transcription	Ovary	ovary
22	chr6:35338800-35350600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:35338800-35353400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:35339000-35351000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:35339200-35340400	Weak transcription	NH-A	brain
26	chr6:35339200-35341000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:35339200-35341400	Enhancers	Brain Substantia Nigra	brain
28	chr6:35339200-35344800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:35339200-35348600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:35339200-35350200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:35339200-35350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:35339200-35353400	Weak transcription	Left Ventricle	heart
33	chr6:35339200-35353400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:35339200-35356600	Weak transcription	Esophagus	oesophagus
35	chr6:35339400-35340400	Weak transcription	NHEK	skin
36	chr6:35339400-35340800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:35339400-35342000	Genic enhancers	Psoas Muscle	Psoas
38	chr6:35339400-35343800	Weak transcription	NHLF	lung
39	chr6:35339400-35345400	Weak transcription	Brain Angular Gyrus	brain
40	chr6:35339400-35346200	Weak transcription	HSMMtube	muscle
41	chr6:35339400-35349400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:35339400-35350800	Weak transcription	Right Atrium	heart
43	chr6:35339400-35353600	Weak transcription	Small Intestine	intestine
44	chr6:35339600-35340400	Weak transcription	Primary T cells from cord blood	blood
45	chr6:35339600-35340600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:35339600-35340600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr6:35339600-35340800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:35339600-35341000	Genic enhancers	Placenta	Placenta
49	chr6:35339600-35342000	Strong transcription	HSMM	muscle
50	chr6:35339600-35343800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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