Variant report

Variant	rs7176849
Chromosome Location	chr15:43681427-43681428
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43681132-43681714	K562	blood:	n/a	n/a
2	POLR2A	chr15:43681263-43681460	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43675492..43679390-chr15:43681135..43683414,3	K562	blood:

Variant related genes	Relation type
TUBGCP4	TF binding region

Extended variants
information (count: 110 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1095386	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11070399	0.92[ASN][1000 genomes]
rs1123947	0.92[ASN][1000 genomes]
rs1133395	0.92[ASN][1000 genomes]
rs11637572	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs11858152	0.90[ASN][1000 genomes]
rs12101673	0.90[ASN][1000 genomes]
rs12102205	0.92[ASN][1000 genomes]
rs12148735	0.81[ASN][1000 genomes]
rs12323999	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324572	0.92[ASN][1000 genomes]
rs12324584	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905772	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs1549523	0.92[ASN][1000 genomes]
rs1549525	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs16957627	0.92[ASN][1000 genomes]
rs16957630	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16957632	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1837959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1837960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012467	0.97[ASN][1000 genomes]
rs2242068	0.91[ASN][1000 genomes]
rs2243434	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2244746	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2264049	0.83[AFR][1000 genomes]
rs2278856	0.92[ASN][1000 genomes]
rs2278857	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs2278859	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2278860	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs2412778	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2412779	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs2412780	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs2412781	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2412782	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439841	0.82[AMR][1000 genomes]
rs2444036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2467733	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2584700	0.89[ASN][1000 genomes]
rs2584701	1.00[ASN][1000 genomes]
rs2584702	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2584703	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28415933	0.92[ASN][1000 genomes]
rs28461955	0.92[ASN][1000 genomes]
rs28653441	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28702649	0.92[ASN][1000 genomes]
rs28729853	0.94[ASN][1000 genomes]
rs2899082	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs3213990	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3213991	0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs3742969	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs3742971	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs3809482	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs4075674	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4296223	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4401024	0.91[ASN][1000 genomes]
rs4547312	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs4583210	0.92[ASN][1000 genomes]
rs471229	0.80[AMR][1000 genomes]
rs478028	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs478104	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs484029	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs484846	0.86[ASN][1000 genomes]
rs488756	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs498837	0.86[ASN][1000 genomes]
rs499035	0.86[ASN][1000 genomes]
rs507178	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs510108	0.86[ASN][1000 genomes]
rs511673	0.91[ASN][1000 genomes]
rs512628	0.91[ASN][1000 genomes]
rs524527	0.91[CHB][hapmap];0.95[YRI][hapmap]
rs526450	0.91[CHB][hapmap];0.95[YRI][hapmap]
rs528517	0.90[ASN][1000 genomes]
rs540031	0.90[ASN][1000 genomes]
rs552701	0.90[ASN][1000 genomes]
rs573615	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs576557	0.83[ASN][1000 genomes]
rs6493081	0.92[ASN][1000 genomes]
rs6493082	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6493083	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6493084	0.92[ASN][1000 genomes]
rs6493085	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6493086	0.92[ASN][1000 genomes]
rs6493087	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs6493088	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs689754	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs7163245	0.94[ASN][1000 genomes]
rs7163288	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7165471	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7166812	0.92[ASN][1000 genomes]
rs7167882	1.00[ASN][1000 genomes]
rs7168940	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7170152	0.92[ASN][1000 genomes]
rs7170489	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs7172374	0.85[ASN][1000 genomes]
rs7175434	0.91[ASN][1000 genomes]
rs8033714	0.88[ASN][1000 genomes]
rs8039638	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs8039671	0.83[AFR][1000 genomes]
rs8041132	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8042688	0.92[ASN][1000 genomes]
rs825739	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs825740	0.87[CHB][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs884704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs933941	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs956391	0.90[ASN][1000 genomes]
rs9920879	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs999026	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7176849	ADAL	cis	Thyroid	GTEx
rs7176849	ADAL	cis	Artery Tibial	GTEx
rs7176849	ADAL	cis	multi-tissue	Pritchard
rs7176849	ADAL	cis	Artery Aorta	GTEx
rs7176849	CATSPER2	cis	Esophagus Mucosa	GTEx
rs7176849	ADAL	cis	lung	GTEx
rs7176849	ADAL	cis	Adipose Subcutaneous	GTEx
rs7176849	ADAL	cis	Esophagus Muscularis	GTEx
rs7176849	CKMT1A	cis	Esophagus Mucosa	GTEx
rs7176849	ADAL	cis	Nerve Tibial	GTEx
rs7176849	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs7176849	ADAL	cis	Skin Sun Exposed Lower leg	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	chr15:43668200-43681800	Strong transcription	Dnd41	blood
12	chr15:43668200-43683800	Strong transcription	Liver	Liver
13	chr15:43668200-43702200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:43668200-43732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:43668400-43683800	Strong transcription	Primary T cells from cord blood	blood
16	chr15:43668600-43681600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:43668600-43681800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:43668600-43681800	Strong transcription	HepG2	liver
19	chr15:43668600-43682000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:43668600-43682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:43668600-43682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:43668800-43681600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr15:43670600-43703200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:43671400-43686600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:43675400-43681800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:43675600-43744400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:43675800-43687000	Weak transcription	NHDF-Ad	bronchial
28	chr15:43676800-43695600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:43677400-43686000	Weak transcription	Fetal Lung	lung
30	chr15:43678000-43687000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:43678200-43686800	Weak transcription	A549	lung
32	chr15:43678200-43686800	Weak transcription	Osteobl	bone
33	chr15:43678200-43688800	Weak transcription	Fetal Brain Male	brain
34	chr15:43678400-43686400	Weak transcription	Gastric	stomach
35	chr15:43678400-43687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:43678400-43688000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:43678400-43689200	Weak transcription	HUVEC	blood vessel
38	chr15:43678400-43693800	Weak transcription	Small Intestine	intestine
39	chr15:43678600-43686000	Weak transcription	Fetal Kidney	kidney
40	chr15:43678600-43686400	Weak transcription	Pancreas	Pancrea
41	chr15:43678600-43686800	Weak transcription	NHEK	skin
42	chr15:43678600-43687200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:43678600-43687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:43678800-43686800	Weak transcription	Colonic Mucosa	Colon
45	chr15:43679200-43686800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:43679600-43683400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr15:43679600-43686600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:43679600-43686800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:43679600-43686800	Weak transcription	HSMMtube	muscle
50	chr15:43679600-43686800	Weak transcription	NH-A	brain

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