Variant report

Variant	rs7164265
Chromosome Location	chr15:51739808-51739809
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	chr15:51734735..51737717-chr15:51738813..51740698,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1031664	0.86[CHB][hapmap]
rs10775144	0.86[CHB][hapmap]
rs1080394	0.81[YRI][hapmap]
rs10851502	1.00[CHB][hapmap];0.91[YRI][hapmap];0.82[ASN][1000 genomes]
rs11070853	0.94[ASN][1000 genomes]
rs11070857	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11070859	0.87[CHB][hapmap];0.81[YRI][hapmap]
rs11070862	0.84[CHB][hapmap]
rs11630336	0.87[ASN][1000 genomes]
rs11630842	0.87[CHB][hapmap]
rs11631408	1.00[CHB][hapmap]
rs11632853	0.90[ASN][1000 genomes]
rs11634110	0.83[ASN][1000 genomes]
rs11634180	0.86[CHB][hapmap];0.86[YRI][hapmap]
rs11635216	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs11635592	0.87[CHB][hapmap]
rs11638240	0.89[ASN][1000 genomes]
rs12101920	0.90[ASN][1000 genomes]
rs12372948	0.86[CHB][hapmap]
rs12438892	1.00[CHB][hapmap];0.84[YRI][hapmap];0.94[ASN][1000 genomes]
rs12440990	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs12443362	0.86[ASN][1000 genomes]
rs12592179	0.91[ASN][1000 genomes]
rs12595672	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12913493	0.93[ASN][1000 genomes]
rs16964357	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs17524813	0.90[ASN][1000 genomes]
rs17603116	0.90[ASN][1000 genomes]
rs17648128	0.83[CEU][hapmap]
rs17648140	0.83[CEU][hapmap]
rs2124592	0.81[YRI][hapmap]
rs2124875	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs2124876	0.82[CHB][hapmap]
rs2414105	0.91[CHB][hapmap]
rs2414106	0.87[CHB][hapmap]
rs2414109	0.87[CHB][hapmap]
rs2414111	0.87[CHB][hapmap]
rs2459396	0.81[CHB][hapmap]
rs28415556	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28431083	0.89[ASN][1000 genomes]
rs28680710	0.90[ASN][1000 genomes]
rs28854610	0.89[ASN][1000 genomes]
rs28878886	0.92[ASN][1000 genomes]
rs4143722	0.89[ASN][1000 genomes]
rs4462537	0.88[ASN][1000 genomes]
rs4774589	0.92[ASN][1000 genomes]
rs4774590	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4774591	0.84[ASN][1000 genomes]
rs4774593	0.90[ASN][1000 genomes]
rs4774597	0.95[CHB][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs4775943	0.86[CHB][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs4775944	0.87[CHB][hapmap]
rs4775946	0.87[CHB][hapmap]
rs4775953	0.87[CHB][hapmap]
rs4775955	0.87[CHB][hapmap]
rs4775960	0.87[CHB][hapmap]
rs4775961	0.87[CHB][hapmap]
rs55981933	0.88[ASN][1000 genomes]
rs56189052	0.90[ASN][1000 genomes]
rs62014659	0.86[ASN][1000 genomes]
rs6493499	0.88[ASN][1000 genomes]
rs6493500	0.88[ASN][1000 genomes]
rs6493501	0.90[ASN][1000 genomes]
rs6493503	0.90[ASN][1000 genomes]
rs6493505	0.87[CHB][hapmap];0.81[YRI][hapmap]
rs67524810	0.89[ASN][1000 genomes]
rs7162412	0.93[ASN][1000 genomes]
rs7162563	0.95[ASN][1000 genomes]
rs7165887	0.87[CHB][hapmap]
rs7170217	0.86[CHB][hapmap];0.85[YRI][hapmap]
rs7170444	0.86[CHB][hapmap];0.83[YRI][hapmap]
rs7174435	0.87[CHB][hapmap]
rs7174495	1.00[CHB][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs7177720	0.87[CHB][hapmap]
rs7181470	0.89[ASN][1000 genomes]
rs8023455	0.84[YRI][hapmap]
rs8024506	0.90[ASN][1000 genomes]
rs8038101	0.84[ASN][1000 genomes]
rs8038341	0.87[ASN][1000 genomes]
rs8039073	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs8042221	0.85[CHB][hapmap]
rs8042289	0.85[CHB][hapmap]
rs882386	0.86[ASN][1000 genomes]
rs930920	0.83[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs9944241	0.87[CHB][hapmap]
rs9944263	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv976935	chr15:51739734-51740998	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7164265	TMOD2	cis	parietal	SCAN
rs7164265	DMXL2	Cis_1M	lymphoblastoid	RTeQTL
rs7164265	LYSMD2	cis	parietal	SCAN
rs7164265	ARPP19	cis	parietal	SCAN
rs7164265	ATP8B4	cis	cerebellum	SCAN
rs7164265	SCG3	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51707400-51740200	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:51731000-51740600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:51732000-51740600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:51732800-51740200	Weak transcription	K562	blood
5	chr15:51733000-51740600	Weak transcription	Brain Anterior Caudate	brain
6	chr15:51733800-51740000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:51734000-51740600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:51734600-51748800	Weak transcription	Fetal Intestine Small	intestine
9	chr15:51734800-51740600	Weak transcription	Lung	lung
10	chr15:51735200-51742000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:51735400-51741200	Weak transcription	Brain Germinal Matrix	brain
12	chr15:51735600-51741000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:51735800-51740600	Weak transcription	Spleen	Spleen
14	chr15:51735800-51742000	Weak transcription	Fetal Kidney	kidney
15	chr15:51736000-51741200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:51736200-51740600	Weak transcription	Fetal Stomach	stomach
17	chr15:51736600-51741400	Weak transcription	Fetal Thymus	thymus
18	chr15:51736800-51751200	Weak transcription	HUVEC	blood vessel
19	chr15:51737000-51740600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:51737000-51775600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:51737000-51776400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:51737200-51741600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:51737400-51740600	Weak transcription	Primary T cells from cord blood	blood
24	chr15:51737400-51740600	Weak transcription	Fetal Lung	lung
25	chr15:51737400-51740600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:51737400-51749000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:51737400-51750200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:51737600-51741600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:51737600-51749200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:51737600-51762400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:51737800-51740600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:51737800-51740600	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:51737800-51741200	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:51737800-51748800	Weak transcription	NHDF-Ad	bronchial
35	chr15:51737800-51758400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:51737800-51762400	Weak transcription	Colonic Mucosa	Colon
37	chr15:51738000-51740200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:51738000-51742000	Weak transcription	NH-A	brain
39	chr15:51738000-51755400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:51738200-51740200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:51738200-51740600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:51738200-51741000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:51738200-51741000	Weak transcription	Dnd41	blood
44	chr15:51738200-51748800	Weak transcription	Fetal Brain Male	brain
45	chr15:51738200-51784600	Weak transcription	Stomach Mucosa	stomach
46	chr15:51738400-51777400	Weak transcription	Small Intestine	intestine
47	chr15:51738600-51741200	Weak transcription	NHLF	lung
48	chr15:51738600-51742600	Strong transcription	Brain Angular Gyrus	brain
49	chr15:51738600-51742600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:51738600-51743400	Strong transcription	Brain Inferior Temporal Lobe	brain

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