Variant report

Variant	rs7170406
Chromosome Location	chr15:30066152-30066153
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	chr15:30055188..30057254-chr15:30065411..30067206,2	K562	blood:
2	chr15:30063787..30066295-chr15:30068795..30070825,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152681	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10519665	1.00[CHB][hapmap]
rs10775231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11073205	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11636849	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[ASN][1000 genomes]
rs12438925	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs12440211	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12440708	0.91[EUR][1000 genomes]
rs12441554	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1383315	0.93[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1480503	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1552077	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs1585900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671556	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs17671580	1.00[CHB][hapmap]
rs2032	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2035326	1.00[CHB][hapmap]
rs2229518	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2291166	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2337167	0.89[CEU][hapmap]
rs2337170	0.84[ASN][1000 genomes]
rs260541	0.84[ASN][1000 genomes]
rs28675809	0.91[EUR][1000 genomes]
rs2878893	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2878905	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3784356	1.00[CHB][hapmap]
rs4073316	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4362339	0.94[CEU][hapmap]
rs4779670	0.94[CEU][hapmap]
rs4780259	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4780260	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4780263	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6495890	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6495914	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6495927	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6495935	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6495945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166786	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168919	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171815	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7175819	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176476	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7176594	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7180387	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs767514	0.93[ASW][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs785445	0.83[CEU][hapmap]
rs785446	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7170406	C15orf2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30016600-30068200	Weak transcription	Brain Germinal Matrix	brain
2	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
3	chr15:30030400-30067000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:30049400-30066400	Weak transcription	Small Intestine	intestine
5	chr15:30050200-30070600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:30052000-30070600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:30052600-30067600	Weak transcription	Stomach Mucosa	stomach
8	chr15:30052600-30089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:30053000-30072600	Weak transcription	Spleen	Spleen
10	chr15:30057400-30067200	Weak transcription	K562	blood
11	chr15:30057600-30068600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:30058000-30067200	Weak transcription	Psoas Muscle	Psoas
13	chr15:30058200-30067200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:30058600-30067200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:30058600-30067200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:30058600-30092200	Weak transcription	Esophagus	oesophagus
17	chr15:30058600-30106000	Weak transcription	Gastric	stomach
18	chr15:30059800-30086200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:30060600-30071200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:30060800-30069200	Weak transcription	Right Atrium	heart
21	chr15:30060800-30076800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:30061000-30067200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:30061200-30066600	Weak transcription	Hela-S3	cervix
24	chr15:30062200-30066400	Weak transcription	NHLF	lung
25	chr15:30062200-30067200	Weak transcription	NHDF-Ad	bronchial
26	chr15:30062400-30072600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:30062800-30096600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:30063000-30072600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:30063600-30066400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:30063600-30066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:30063600-30067400	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:30063600-30069000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:30063600-30072600	Weak transcription	Lung	lung
34	chr15:30063600-30073400	Weak transcription	Fetal Lung	lung
35	chr15:30063800-30066400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:30063800-30066400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:30063800-30067200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:30063800-30067200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:30063800-30067200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:30063800-30067200	Weak transcription	HSMMtube	muscle
41	chr15:30063800-30067400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:30063800-30068800	Weak transcription	Liver	Liver
43	chr15:30063800-30069000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:30063800-30070400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:30063800-30070800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:30063800-30071000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:30063800-30076800	Weak transcription	Fetal Kidney	kidney
48	chr15:30063800-30096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr15:30063800-30096800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr15:30064000-30069200	Weak transcription	Ovary	ovary

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