Variant report

Variant	rs7167882
Chromosome Location	chr15:43678663-43678664
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43671018..43673018-chr15:43678114..43680369,2	K562	blood:
2	chr15:43662885..43665399-chr15:43678484..43680491,2	MCF-7	breast:
3	chr15:43675492..43679390-chr15:43681135..43683414,3	K562	blood:

Variant related genes	Relation type
ENSG00000137822	Chromatin interaction
ENSG00000140265	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1058298	0.85[EUR][1000 genomes]
rs1060939	0.80[AMR][1000 genomes]
rs1079309	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1095386	0.90[ASN][1000 genomes]
rs11070399	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1123947	0.92[ASN][1000 genomes]
rs1133395	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637572	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858152	0.90[ASN][1000 genomes]
rs12101673	0.90[ASN][1000 genomes]
rs12102205	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12148735	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12323999	1.00[ASN][1000 genomes]
rs12324572	0.92[ASN][1000 genomes]
rs12324584	1.00[ASN][1000 genomes]
rs12905772	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549523	0.92[ASN][1000 genomes]
rs1549525	0.92[ASN][1000 genomes]
rs16957627	0.92[ASN][1000 genomes]
rs16957630	0.92[ASN][1000 genomes]
rs16957632	0.92[ASN][1000 genomes]
rs1837959	0.94[ASN][1000 genomes]
rs1837960	0.94[ASN][1000 genomes]
rs1869258	0.84[AMR][1000 genomes]
rs2012467	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242068	0.91[ASN][1000 genomes]
rs2243434	0.96[ASN][1000 genomes]
rs2244746	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2244981	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2249952	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2253268	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2253807	0.87[AMR][1000 genomes]
rs2264050	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278856	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278857	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278859	0.92[ASN][1000 genomes]
rs2278860	0.92[ASN][1000 genomes]
rs2412778	0.92[ASN][1000 genomes]
rs2412779	0.92[ASN][1000 genomes]
rs2412780	0.92[ASN][1000 genomes]
rs2412781	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412782	0.97[ASN][1000 genomes]
rs2439845	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2439846	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2444036	0.97[ASN][1000 genomes]
rs2444037	0.88[EUR][1000 genomes]
rs2444251	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2467733	0.97[ASN][1000 genomes]
rs2467737	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2467738	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2467741	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2467742	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2467745	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2584700	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2584701	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2584702	1.00[ASN][1000 genomes]
rs2584703	0.94[ASN][1000 genomes]
rs2584727	0.80[AMR][1000 genomes]
rs2602141	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28415933	0.92[ASN][1000 genomes]
rs28461955	0.92[ASN][1000 genomes]
rs28649346	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28653441	0.97[ASN][1000 genomes]
rs28702649	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28729853	0.94[ASN][1000 genomes]
rs2899082	0.92[ASN][1000 genomes]
rs2924369	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3213990	0.95[ASN][1000 genomes]
rs3213991	0.96[ASN][1000 genomes]
rs3742969	0.91[ASN][1000 genomes]
rs3742971	0.91[ASN][1000 genomes]
rs3809482	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4075674	0.92[ASN][1000 genomes]
rs4296223	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4401024	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547312	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4583210	0.92[ASN][1000 genomes]
rs478028	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478104	0.85[ASN][1000 genomes]
rs480108	0.80[AMR][1000 genomes]
rs484029	0.91[ASN][1000 genomes]
rs484846	0.86[ASN][1000 genomes]
rs485148	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs488756	0.90[ASN][1000 genomes]
rs491800	0.86[EUR][1000 genomes]
rs493377	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs498837	0.86[ASN][1000 genomes]
rs499035	0.86[ASN][1000 genomes]
rs506120	0.82[AMR][1000 genomes]
rs507178	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs509306	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs510108	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs511673	0.91[ASN][1000 genomes]
rs512628	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs518288	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs528517	0.90[ASN][1000 genomes]
rs529611	0.81[AMR][1000 genomes]
rs536313	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs538238	0.83[EUR][1000 genomes]
rs540031	0.90[ASN][1000 genomes]
rs542898	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs548704	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs552701	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs560191	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs572837	0.80[AMR][1000 genomes]
rs573615	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576557	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493081	0.92[ASN][1000 genomes]
rs6493082	0.92[ASN][1000 genomes]
rs6493083	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493084	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493085	0.92[ASN][1000 genomes]
rs6493086	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493087	0.81[ASN][1000 genomes]
rs6493088	0.96[ASN][1000 genomes]
rs689693	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs689767	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs690012	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs690276	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690367	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690446	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690472	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690512	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs693510	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs694725	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163245	0.94[ASN][1000 genomes]
rs7165471	0.92[ASN][1000 genomes]
rs7166812	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168940	0.90[ASN][1000 genomes]
rs7170152	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7170489	0.92[ASN][1000 genomes]
rs7172374	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175434	0.91[ASN][1000 genomes]
rs7176849	1.00[ASN][1000 genomes]
rs7497780	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8033714	0.88[ASN][1000 genomes]
rs8039638	0.90[ASN][1000 genomes]
rs8041132	0.92[ASN][1000 genomes]
rs8042688	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs825739	0.81[ASN][1000 genomes]
rs825740	0.81[ASN][1000 genomes]
rs884704	0.98[ASN][1000 genomes]
rs933941	0.92[ASN][1000 genomes]
rs956391	0.90[ASN][1000 genomes]
rs9920879	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs999026	0.97[ASN][1000 genomes]
rs999047	0.97[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	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	esv3449979	chr15:43677710-43679708	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7167882	TGM5	cis	multi-tissue	Pritchard
rs7167882	ZSCAN29	cis	Thyroid	GTEx
rs7167882	STRCP1	cis	Esophagus Muscularis	GTEx
rs7167882	TGM7	cis	Esophagus Mucosa	GTEx
rs7167882	ADAL	cis	Nerve Tibial	GTEx
rs7167882	ZSCAN29	cis	multi-tissue	Pritchard
rs7167882	AC011330.5	cis	Artery Tibial	GTEx
rs7167882	AC011330.5	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43664000-43692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:43664600-43687800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:43664600-43688000	Weak transcription	Stomach Mucosa	stomach
4	chr15:43664600-43695600	Weak transcription	Fetal Heart	heart
5	chr15:43665000-43687800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:43665000-43730000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:43665200-43686600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:43667400-43681600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:43667600-43681600	Strong transcription	Hela-S3	cervix
10	chr15:43668000-43717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:43668200-43680400	Strong transcription	Fetal Stomach	stomach
12	chr15:43668200-43680600	Strong transcription	Fetal Muscle Leg	muscle
13	chr15:43668200-43680800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:43668200-43681400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr15:43668200-43681800	Strong transcription	Dnd41	blood
16	chr15:43668200-43683800	Strong transcription	Liver	Liver
17	chr15:43668200-43702200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:43668200-43732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:43668400-43679600	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr15:43668400-43680600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:43668400-43680800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr15:43668400-43683800	Strong transcription	Primary T cells from cord blood	blood
23	chr15:43668600-43679600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:43668600-43680800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:43668600-43680800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:43668600-43681200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:43668600-43681400	Strong transcription	Primary hematopoietic stem cells	blood
28	chr15:43668600-43681400	Strong transcription	Fetal Thymus	thymus
29	chr15:43668600-43681600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:43668600-43681800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:43668600-43681800	Strong transcription	HepG2	liver
32	chr15:43668600-43682000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:43668600-43682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:43668600-43682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:43668800-43678800	Strong transcription	Primary B cells from cord blood	blood
36	chr15:43668800-43679200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:43668800-43680400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:43668800-43680800	Strong transcription	Adipose Nuclei	Adipose
39	chr15:43668800-43681200	Strong transcription	Fetal Intestine Large	intestine
40	chr15:43668800-43681400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr15:43668800-43681400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr15:43668800-43681400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr15:43668800-43681600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:43669000-43680600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:43669000-43681400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:43669200-43681000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:43669200-43681400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:43670600-43703200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:43671400-43686600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:43671600-43680600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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