Variant report

Variant	rs10470412
Chromosome Location	chr3:121613054-121613055
allele	C/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	SP1	chr3:121613027-121613818	H1-hESC	embryonic stem cell:	n/a	n/a
2	NFIC	chr3:121613027-121613970	ECC-1	luminal epithelium:	n/a	chr3:121613718-121613735
3	POLR2A	chr3:121613023-121613830	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFIC	chr3:121613048-121613933	ECC-1	luminal epithelium:	n/a	chr3:121613718-121613735

Variant related genes	Relation type
SLC15A2	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10470411	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511407	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10934561	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs11713268	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919421	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs12486309	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12486310	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12486456	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs12487516	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488692	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489142	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489686	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12491109	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12492214	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs12492861	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12493270	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634458	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636562	1.00[CEU][hapmap]
rs12695417	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077143	0.86[AFR][1000 genomes]
rs13100245	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881997	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881998	0.91[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];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920307	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];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920310	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2222826	0.87[EUR][1000 genomes]
rs2293613	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.88[YRI][hapmap]
rs2689274	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689279	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689280	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2689286	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700412	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700413	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]
rs2700414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700419	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28844130	0.87[EUR][1000 genomes]
rs34241542	0.87[EUR][1000 genomes]
rs35354585	0.87[EUR][1000 genomes]
rs35692621	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35723704	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3805125	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3805129	0.90[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3805132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4048630	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271411	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602434	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4603998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610269	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4676760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4676762	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55653962	0.91[AFR][1000 genomes]
rs55955745	0.91[AFR][1000 genomes]
rs56408673	0.91[AFR][1000 genomes]
rs57365001	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57473053	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58485759	0.87[EUR][1000 genomes]
rs59064186	0.87[EUR][1000 genomes]
rs61567016	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798575	0.91[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs72959293	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72961314	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619918	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620562	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625960	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627291	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643293	1.00[CEU][hapmap]
rs7647585	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650341	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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818733	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831798	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832735	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865926	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882841	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv877384	chr3:121601577-121659774	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10470412	PARP14	cis	cerebellum	SCAN
rs10470412	HCLS1	cis	multi-tissue	Pritchard
rs10470412	HCLS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121555800-121615600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:121559200-121613200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:121585000-121613200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:121592800-121646800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:121593000-121615400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:121593000-121632400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:121604600-121613200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:121604600-121613400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:121604600-121613400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:121605200-121613800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:121610600-121621800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:121612200-121613200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:121612200-121613200	Enhancers	Fetal Muscle Leg	muscle
14	chr3:121612200-121614200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:121612400-121616000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:121612800-121613200	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr3:121612800-121613400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:121612800-121613400	Enhancers	Pancreas	Pancrea
19	chr3:121612800-121613600	Enhancers	Psoas Muscle	Psoas
20	chr3:121612800-121613800	Enhancers	Placenta	Placenta
21	chr3:121612800-121614000	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:121612800-121614800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:121612800-121615000	Active TSS	Fetal Muscle Trunk	muscle
24	chr3:121613000-121613200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:121613000-121613200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:121613000-121613200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:121613000-121613200	Enhancers	Adipose Nuclei	Adipose
28	chr3:121613000-121613200	Active TSS	Brain Substantia Nigra	brain
29	chr3:121613000-121613200	Enhancers	Colon Smooth Muscle	Colon
30	chr3:121613000-121613200	Enhancers	Fetal Kidney	kidney
31	chr3:121613000-121613200	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:121613000-121613200	Active TSS	HSMMtube	muscle
33	chr3:121613000-121613400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:121613000-121613400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:121613000-121613400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:121613000-121613400	Active TSS	Brain Hippocampus Middle	brain
37	chr3:121613000-121613400	Enhancers	Fetal Brain Female	brain
38	chr3:121613000-121613600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:121613000-121613600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr3:121613000-121613600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:121613000-121613600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr3:121613000-121613800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr3:121613000-121614200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr3:121613000-121614200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:121613000-121614200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr3:121613000-121614200	Active TSS	Brain Anterior Caudate	brain
47	chr3:121613000-121614200	Active TSS	Brain Cingulate Gyrus	brain
48	chr3:121613000-121614200	Enhancers	Fetal Heart	heart
49	chr3:121613000-121614200	Enhancers	Fetal Lung	lung
50	chr3:121613000-121614200	Enhancers	Skeletal Muscle Male	skeletal muscle

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