Variant report

Variant	rs7164339
Chromosome Location	chr15:41025275-41025276
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	chr15:41024400..41027311-chr15:41063021..41065498,2	K562	blood:
2	chr15:40919306..40921554-chr15:41023722..41025416,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10775121	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070291	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070293	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11631563	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11633269	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11852786	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855560	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11858337	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11858338	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12372947	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12439683	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441514	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12442845	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12593359	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908284	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2263551	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2304582	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2412546	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412547	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412548	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412549	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2577564	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2619679	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2619680	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2619683	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2917955	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2928140	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3092982	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3092983	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3101861	0.88[EUR][1000 genomes]
rs34400306	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36106105	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45495293	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4923884	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924493	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924495	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924501	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924503	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56042757	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6492961	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167854	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7169010	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7172195	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7173646	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7174551	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7175401	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs752012	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8025883	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8033829	0.88[EUR][1000 genomes]
rs8036817	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7164339	C15orf57	cis	Artery Aorta	GTEx
rs7164339	C15orf57	cis	Nerve Tibial	GTEx
rs7164339	C15orf57	cis	Artery Tibial	GTEx
rs7164339	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs7164339	C15orf57	cis	lung	GTEx
rs7164339	RP11-111A22.1	cis	lung	GTEx
rs7164339	RP11-111A22.1	cis	Artery Tibial	GTEx
rs7164339	C15orf57	cis	Esophagus Muscularis	GTEx
rs7164339	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs7164339	C15orf57	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
4	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
7	chr15:40999000-41027600	Weak transcription	Gastric	stomach
8	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:41012800-41028200	Weak transcription	NHLF	lung
11	chr15:41014600-41029600	Weak transcription	Esophagus	oesophagus
12	chr15:41016600-41027400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:41019200-41035600	Weak transcription	Fetal Heart	heart
14	chr15:41019400-41028600	Weak transcription	Fetal Brain Male	brain
15	chr15:41019400-41036000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:41019400-41046200	Strong transcription	Fetal Stomach	stomach
17	chr15:41019600-41027000	Weak transcription	Small Intestine	intestine
18	chr15:41019600-41036200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:41019600-41036200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:41020000-41026200	Weak transcription	Lung	lung
21	chr15:41020000-41027800	Weak transcription	Psoas Muscle	Psoas
22	chr15:41020000-41029800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr15:41020000-41036000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:41020000-41043600	Strong transcription	Dnd41	blood
25	chr15:41020200-41027800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:41020200-41030600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:41020400-41026000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:41020400-41026600	Weak transcription	Brain Anterior Caudate	brain
29	chr15:41020400-41027200	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:41020400-41027600	Weak transcription	Left Ventricle	heart
31	chr15:41020400-41027800	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:41020400-41028000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:41020400-41028200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:41020400-41028200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:41020400-41035600	Strong transcription	K562	blood
36	chr15:41020400-41035800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:41020400-41036000	Strong transcription	Fetal Thymus	thymus
38	chr15:41020400-41037600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr15:41020600-41029600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:41020600-41030800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:41020600-41030800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:41020600-41033600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:41020600-41036000	Strong transcription	Placenta	Placenta
44	chr15:41020600-41036800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:41020600-41037800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr15:41020600-41038200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr15:41020800-41027200	Strong transcription	Hela-S3	cervix
48	chr15:41020800-41032600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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