Variant report

Variant	rs2291449
Chromosome Location	chr15:76579234-76579235
allele	A/G
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	chr15:76579146-76579341	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr15:76579123-76579349	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76579019..76580557-chr15:76600815..76603366,2	K562	blood:
2	chr15:76577736..76580355-chr15:76602966..76605157,2	MCF-7	breast:

Variant related genes	Relation type
ETFA	TF binding region
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12905758	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs17456573	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1801591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810348	0.87[CEU][hapmap]
rs1914816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2255408	0.85[ASN][1000 genomes]
rs2456027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2456033	0.89[ASN][1000 genomes]
rs2456040	1.00[ASN][1000 genomes]
rs2456042	1.00[ASN][1000 genomes]
rs2456047	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs2456051	0.89[CHD][hapmap]
rs2456063	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2456066	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2456067	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456070	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2456072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2456074	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456075	0.96[ASN][1000 genomes]
rs2456078	0.96[ASN][1000 genomes]
rs2460146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2460151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2460153	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2460155	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2460158	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2469211	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2469212	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469214	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469216	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469533	0.85[ASN][1000 genomes]
rs2469538	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469539	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469544	0.89[ASN][1000 genomes]
rs2469552	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469559	0.89[CHD][hapmap];1.00[MEX][hapmap]
rs2469564	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2469568	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2469573	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2938691	0.96[ASN][1000 genomes]
rs2956875	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2957037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2959846	1.00[ASN][1000 genomes]
rs4886490	0.86[CEU][hapmap]
rs6495200	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67241126	1.00[AFR][1000 genomes]
rs8042255	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874224	0.87[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2291449	HPCA	trans	brain	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76555800-76586000	Weak transcription	Stomach Mucosa	stomach
2	chr15:76556400-76581400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:76556800-76594600	Weak transcription	Esophagus	oesophagus
4	chr15:76557000-76582800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
6	chr15:76560000-76582400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:76561000-76580400	Strong transcription	Adipose Nuclei	Adipose
8	chr15:76561000-76587600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:76562000-76591600	Weak transcription	Small Intestine	intestine
10	chr15:76562600-76586000	Weak transcription	Brain Angular Gyrus	brain
11	chr15:76562800-76580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:76563000-76581800	Weak transcription	Fetal Brain Male	brain
13	chr15:76563000-76586400	Weak transcription	Fetal Heart	heart
14	chr15:76563200-76590800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:76564200-76580600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:76565200-76581200	Strong transcription	HepG2	liver
17	chr15:76565200-76581400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:76566400-76579600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:76567600-76581800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:76568800-76581600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:76569000-76580600	Strong transcription	Osteobl	bone
22	chr15:76569000-76585200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:76569000-76586400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:76569200-76580400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:76569200-76581400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr15:76569200-76581600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:76569400-76579800	Strong transcription	Fetal Lung	lung
28	chr15:76569400-76580400	Strong transcription	Fetal Muscle Leg	muscle
29	chr15:76569400-76583600	Strong transcription	Hela-S3	cervix
30	chr15:76569400-76585000	Strong transcription	Fetal Intestine Large	intestine
31	chr15:76569800-76591600	Weak transcription	Spleen	Spleen
32	chr15:76570000-76580000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:76570800-76581400	Weak transcription	Fetal Brain Female	brain
34	chr15:76571200-76586400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:76572000-76580400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:76572000-76581600	Strong transcription	Placenta	Placenta
37	chr15:76572600-76585800	Weak transcription	Brain Anterior Caudate	brain
38	chr15:76573200-76592200	Weak transcription	Fetal Kidney	kidney
39	chr15:76573200-76593200	Weak transcription	Right Ventricle	heart
40	chr15:76573600-76580400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:76574200-76580400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:76574400-76580200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:76574600-76579600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:76574600-76580400	Strong transcription	K562	blood
45	chr15:76574600-76585200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:76574800-76582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:76574800-76590600	Weak transcription	Ovary	ovary
48	chr15:76574800-76591600	Weak transcription	Gastric	stomach
49	chr15:76574800-76591600	Weak transcription	Lung	lung
50	chr15:76574800-76601400	Weak transcription	Pancreas	Pancrea

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