Variant report

Variant	rs7166105
Chromosome Location	chr15:75343942-75343943
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	chr15:75337101..75339665-chr15:75342536..75344490,2	MCF-7	breast:
2	chr15:75343146..75345487-chr15:75493185..75495444,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11072519	0.82[CEU][hapmap]
rs12148355	0.81[ASN][1000 genomes]
rs12591175	0.85[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12591994	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592477	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12593542	0.82[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs12594117	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289582	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2304904	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28394281	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743212	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs3812943	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3812946	0.82[EUR][1000 genomes]
rs3816261	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850093	0.81[ASW][hapmap];0.85[LWK][hapmap]
rs3910748	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55877218	0.84[AMR][1000 genomes]
rs56828495	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56970592	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58068887	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58294763	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58403754	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58645417	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59094290	0.81[ASN][1000 genomes]
rs59303424	0.99[ASN][1000 genomes]
rs61166993	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495135	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495136	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495137	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495138	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495140	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495142	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495146	0.99[ASN][1000 genomes]
rs6495148	0.96[ASN][1000 genomes]
rs7163390	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs7167415	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7168638	0.81[AMR][1000 genomes]
rs7172065	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7172715	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7172989	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7173218	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7174129	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7175720	0.91[LWK][hapmap]
rs7177109	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7179097	0.84[AMR][1000 genomes]
rs7181942	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182286	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72475969	0.99[ASN][1000 genomes]
rs7342591	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7342601	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73432941	0.98[ASN][1000 genomes]
rs73436579	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73436586	0.84[EUR][1000 genomes]
rs73438537	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73438554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73438569	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74023908	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74023935	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74023936	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs74025863	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8024931	0.93[ASN][1000 genomes]
rs8031545	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8033125	0.96[ASN][1000 genomes]
rs8034149	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8036573	0.81[ASN][1000 genomes]
rs8038365	0.97[ASN][1000 genomes]
rs8039433	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs8040961	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9672926	0.83[EUR][1000 genomes]
rs9672995	0.80[ASN][1000 genomes]
rs9672996	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9673012	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9788648	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7166105	SCAMP5	cis	lymphoblastoid	seeQTL
rs7166105	SCAMP5	cis	Esophagus Mucosa	GTEx
rs7166105	SCAMP5	cis	Artery Tibial	GTEx
rs7166105	PPCDC	cis	Adipose Subcutaneous	GTEx
rs7166105	SCAMP5	cis	Thyroid	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:75329400-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:75334000-75344600	Enhancers	Placenta	Placenta
5	chr15:75334200-75344600	Enhancers	Right Ventricle	heart
6	chr15:75334800-75344600	Enhancers	Left Ventricle	heart
7	chr15:75335200-75344200	Enhancers	Fetal Lung	lung
8	chr15:75336000-75350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:75337200-75353600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:75338800-75344000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:75339600-75344000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:75339600-75344400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:75339600-75351800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:75339800-75344000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:75339800-75344600	Genic enhancers	Fetal Stomach	stomach
16	chr15:75339800-75346400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:75340000-75344000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:75340000-75344600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:75340000-75350400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:75340000-75350600	Weak transcription	NH-A	brain
21	chr15:75340000-75350600	Weak transcription	Osteobl	bone
22	chr15:75340000-75353400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:75340000-75353400	Weak transcription	NHDF-Ad	bronchial
24	chr15:75340000-75360600	Weak transcription	Gastric	stomach
25	chr15:75340200-75345800	Weak transcription	NHLF	lung
26	chr15:75340200-75350200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:75340200-75350400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:75340200-75350600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:75340200-75351800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:75340200-75353000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:75340200-75353600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:75340200-75359400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:75340400-75344600	Strong transcription	Fetal Intestine Small	intestine
34	chr15:75340400-75346000	Weak transcription	K562	blood
35	chr15:75340400-75350200	Weak transcription	HMEC	breast
36	chr15:75340400-75353800	Weak transcription	Liver	Liver
37	chr15:75340600-75344000	Weak transcription	HepG2	liver
38	chr15:75340600-75346200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:75340800-75344000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:75340800-75344600	Genic enhancers	Fetal Muscle Leg	muscle
41	chr15:75340800-75345600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:75340800-75346000	Weak transcription	HUVEC	blood vessel
43	chr15:75340800-75357600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:75341000-75356400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:75341200-75357800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:75341400-75344800	Weak transcription	Primary B cells from cord blood	blood
47	chr15:75341400-75346200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:75341600-75344000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:75341600-75345200	Weak transcription	Stomach Mucosa	stomach
50	chr15:75341600-75350800	Weak transcription	A549	lung

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