Variant report

Variant	rs10917876
Chromosome Location	chr1:161736706-161736707
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	STAT3	chr1:161735779-161736764	GM12878	blood:	n/a	chr1:161736288-161736296
2	MXI1	chr1:161734401-161736955	SK-N-SH	brain:	n/a	n/a
3	USF2	chr1:161735862-161736857	Hela-S3	cervix:	n/a	n/a
4	SPI1	chr1:161735866-161736748	HL-60	blood:	n/a	n/a
5	MTA3	chr1:161735688-161736773	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:161735009-161736873	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:161735708-161737161	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:161736654-161736736	Hela-S3	cervix:	n/a	n/a
9	BHLHE40	chr1:161735744-161736790	GM12878	blood:	n/a	n/a
10	MXI1	chr1:161735775-161736796	GM12878	blood:	n/a	n/a
11	MAX	chr1:161735720-161736712	HCT-116	colon:	n/a	n/a
12	POLR2A	chr1:161735702-161736844	Hela-S3	cervix:	n/a	n/a
13	CBX3	chr1:161735772-161736769	HCT-116	colon:	n/a	n/a
14	MXI1	chr1:161734866-161736880	IMR90	lung:	n/a	n/a
15	CHD1	chr1:161735041-161736736	GM12878	blood:	n/a	n/a
16	REST	chr1:161735698-161736728	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr1:161735753-161736729	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:161735022-161736807	MCF10A-Er-Src	breast:	n/a	n/a
19	RUNX3	chr1:161735805-161736766	GM12878	blood:	n/a	n/a
20	CREB1	chr1:161735741-161736807	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:161735780-161736842	GM12878	blood:	n/a	n/a
22	JUN	chr1:161735536-161736884	K562	blood:	n/a	n/a
23	GATA3	chr1:161736641-161736929	SH-SY5Y	brain:	n/a	n/a
24	CREB1	chr1:161735631-161736708	GM12878	blood:	n/a	n/a
25	MAX	chr1:161735849-161736706	Hela-S3	cervix:	n/a	n/a
26	MYC	chr1:161736567-161736722	MCF10A-Er-Src	breast:	n/a	n/a
27	SIN3AK20	chr1:161735695-161736730	HCT-116	colon:	n/a	n/a
28	POLR2A	chr1:161735787-161736856	GM12892	blood:	n/a	n/a
29	NFYB	chr1:161736538-161737051	GM12878	blood:	n/a	n/a
30	POU2F2	chr1:161735733-161736758	GM12878	blood:	n/a	n/a
31	MYC	chr1:161735775-161736770	K562	blood:	n/a	n/a
32	GTF2F1	chr1:161735801-161736772	Hela-S3	cervix:	n/a	n/a
33	HCFC1	chr1:161734711-161737545	Hela-S3	cervix:	n/a	n/a
34	YY1	chr1:161735846-161736737	GM12878	blood:	n/a	chr1:161736538-161736548 chr1:161736537-161736545
35	POLR2A	chr1:161735065-161736712	PBDE	blood:	n/a	n/a
36	RUNX3	chr1:161735706-161736843	GM12878	blood:	n/a	n/a
37	RFX5	chr1:161734956-161736789	Hela-S3	cervix:	n/a	n/a
38	YY1	chr1:161735872-161736753	GM12892	blood:	n/a	chr1:161736538-161736548 chr1:161736537-161736545
39	YY1	chr1:161735837-161736725	GM12878	blood:	n/a	chr1:161736538-161736548 chr1:161736537-161736545
40	HA-E2F1	chr1:161735992-161736736	MCF-7	breast:	n/a	chr1:161736093-161736103 chr1:161736551-161736558
41	POLR2A	chr1:161735125-161736726	IMR90	lung:	n/a	n/a
42	POLR2A	chr1:161735775-161736809	GM12892	blood:	n/a	n/a
43	EP300	chr1:161735728-161736795	GM12878	blood:	n/a	chr1:161736096-161736105
44	POLR2A	chr1:161735722-161736759	GM12891	blood:	n/a	n/a
45	TCF12	chr1:161735668-161736711	A549	lung:	n/a	n/a
46	POLR2A	chr1:161735762-161736779	GM12878	blood:	n/a	n/a
47	SP1	chr1:161735648-161736743	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
2	chr1:161736307..161736956-chr6:36561688..36562628,2	Hela-S3	cervix:
3	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
4	chr1:161736130..161736806-chr2:38977949..38978646,2	Hela-S3	cervix:
5	chr1:161736100..161738231-chr1:161757692..161759293,2	MCF-7	breast:
6	chr1:161736308..161738165-chr1:161740063..161741622,2	MCF-7	breast:
7	chr1:161736283..161737059-chrX:40869502..40870075,2	Hela-S3	cervix:
8	chr1:161718427..161720383-chr1:161735445..161737521,2	MCF-7	breast:
9	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226889	TF binding region
ENSG00000081721	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10436881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10494357	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1063179	0.85[CHB][hapmap]
rs10800032	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800079	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10917968	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10918029	0.92[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs12042663	0.80[ASN][1000 genomes]
rs12045320	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12078104	0.85[CHB][hapmap]
rs12081397	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12086247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12097712	0.84[ASN][1000 genomes]
rs12691498	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs1394066	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1503815	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1875762	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28628087	0.81[EUR][1000 genomes]
rs3767636	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767637	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60578284	0.84[ASN][1000 genomes]
rs6427632	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6660014	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6672073	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6698956	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7355188	0.80[ASN][1000 genomes]
rs7516955	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7518743	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10917876	DUSP12	cis	lymphoblastoid	seeQTL
rs10917876	NCSTN	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161733600-161737000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:161733800-161737400	Active TSS	A549	lung
3	chr1:161734600-161736800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:161734600-161736800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:161734600-161736800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:161734600-161736800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:161734600-161736800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:161734600-161736800	Active TSS	Fetal Intestine Large	intestine
9	chr1:161734600-161736800	Active TSS	Fetal Kidney	kidney
10	chr1:161734600-161736800	Active TSS	Fetal Muscle Leg	muscle
11	chr1:161734600-161736800	Active TSS	Fetal Stomach	stomach
12	chr1:161734600-161736800	Active TSS	HSMM	muscle
13	chr1:161734600-161736800	Active TSS	HSMMtube	muscle
14	chr1:161734600-161736800	Active TSS	HUVEC	blood vessel
15	chr1:161734600-161736800	Active TSS	NHDF-Ad	bronchial
16	chr1:161734600-161736800	Active TSS	NHEK	skin
17	chr1:161734600-161737000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr1:161734600-161737000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:161734600-161737000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:161734600-161737000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:161734600-161737000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:161734600-161737000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:161734600-161737000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:161734600-161737000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:161734600-161737000	Active TSS	Aorta	Aorta
26	chr1:161734600-161737000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:161734600-161737000	Active TSS	Ovary	ovary
28	chr1:161734600-161737000	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:161734600-161737000	Active TSS	GM12878-XiMat	blood
30	chr1:161734600-161737000	Active TSS	NHLF	lung
31	chr1:161734600-161737200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:161734600-161737200	Active TSS	Right Ventricle	heart
33	chr1:161734600-161737400	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr1:161734600-161737600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:161734800-161736800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:161734800-161736800	Active TSS	Colonic Mucosa	Colon
37	chr1:161734800-161736800	Active TSS	HMEC	breast
38	chr1:161734800-161737000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:161734800-161737000	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr1:161734800-161737000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:161734800-161737000	Active TSS	Fetal Brain Female	brain
42	chr1:161734800-161737000	Active TSS	Fetal Intestine Small	intestine
43	chr1:161734800-161737000	Active TSS	Left Ventricle	heart
44	chr1:161734800-161737200	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:161734800-161737200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:161734800-161737200	Active TSS	Psoas Muscle	Psoas
47	chr1:161735000-161736800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:161735000-161736800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:161735000-161736800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:161735000-161737000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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