Variant report

Variant	rs11716116
Chromosome Location	chr3:19989504-19989505
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	CTCF	chr3:19989480-19989630	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:19988773-19989680	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:19987362-19989595	K562	blood:	n/a	n/a
4	HCFC1	chr3:19987605-19989689	K562	blood:	n/a	n/a
5	RUNX3	chr3:19987795-19989519	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:19987558-19989602	GM18951	blood:	n/a	n/a
7	POLR2A	chr3:19986887-19989909	GM12891	blood:	n/a	n/a
8	STAT1	chr3:19987955-19989668	GM12878	blood:	n/a	chr3:19988530-19988542 chr3:19989252-19989264 chr3:19989188-19989197 chr3:19988321-19988329 chr3:19989110-19989122
9	FOS	chr3:19989068-19989592	MCF10A-Er-Src	breast:	n/a	chr3:19989188-19989197 chr3:19989189-19989198 chr3:19989190-19989201 chr3:19989187-19989199 chr3:19989188-19989198 chr3:19989187-19989198
10	SIN3AK20	chr3:19987338-19989938	MCF-7	breast:	n/a	n/a
11	EP300	chr3:19988051-19989533	GM12878	blood:	n/a	chr3:19989189-19989198 chr3:19988330-19988346 chr3:19988621-19988637
12	HEY1	chr3:19987858-19989594	K562	blood:	n/a	n/a
13	CREB1	chr3:19988089-19989745	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:19988117-19989553	MCF-7	breast:	n/a	n/a
15	MAX	chr3:19987921-19989653	HepG2	liver:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
16	SMARCC1	chr3:19986964-19989766	Hela-S3	cervix:	n/a	chr3:19989188-19989197 chr3:19989189-19989198
17	SIN3AK20	chr3:19988033-19989755	K562	blood:	n/a	n/a
18	POLR2A	chr3:19987474-19989718	GM12878	blood:	n/a	n/a
19	MAX	chr3:19988142-19989678	MCF-7	breast:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
20	MYC	chr3:19988199-19989610	MCF10A-Er-Src	breast:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
21	CUX1	chr3:19989021-19990564	K562	blood:	n/a	n/a
22	POLR2A	chr3:19987476-19989652	U87	brain:	n/a	n/a
23	POLR2A	chr3:19987594-19989784	GM18505	blood:	n/a	n/a
24	HMGN3	chr3:19987829-19989561	K562	blood:	n/a	chr3:19989190-19989199
25	HEY1	chr3:19989172-19989595	HepG2	liver:	n/a	n/a
26	YY1	chr3:19988002-19989624	NT2-D1	testis:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19988151-19988159 chr3:19989258-19989280
27	POLR2A	chr3:19987565-19989776	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:19987429-19989814	H1-hESC	embryonic stem cell:	n/a	n/a
29	TBP	chr3:19986938-19989974	K562	blood:	n/a	n/a
30	CTCF	chr3:19989440-19989590	MCF-7	breast:	n/a	chr3:19989472-19989480
31	YY1	chr3:19987910-19989745	K562	blood:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19987999-19988008 chr3:19988151-19988159 chr3:19989258-19989280
32	TAF1	chr3:19987973-19989612	H1-neurons	neurons:	n/a	n/a
33	WRNIP1	chr3:19987590-19989775	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:19987007-19989845	K562	blood:	n/a	n/a
35	YY1	chr3:19988848-19989527	GM12891	blood:	n/a	chr3:19989269-19989277 chr3:19989258-19989280
36	E2F4	chr3:19987975-19989588	K562	blood:	n/a	chr3:19988690-19988700 chr3:19987999-19988008 chr3:19988611-19988620 chr3:19987996-19988008 chr3:19988615-19988625
37	POLR2A	chr3:19986884-19989655	Hela-S3	cervix:	n/a	n/a
38	MAFK	chr3:19988897-19990057	Hela-S3	cervix:	n/a	chr3:19989882-19989896 chr3:19989888-19989899 chr3:19989881-19989897 chr3:19989884-19989899 chr3:19989879-19989899
39	YY1	chr3:19987942-19989572	K562	blood:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19987999-19988008 chr3:19988151-19988159 chr3:19989258-19989280
40	POLR2A	chr3:19986589-19991063	MCF10A-Er-Src	breast:	n/a	n/a
41	TBP	chr3:19989398-19989688	GM12878	blood:	n/a	n/a
42	YY1	chr3:19988026-19989576	HepG2	liver:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19988151-19988159 chr3:19989258-19989280
43	GATA1	chr3:19987428-19990353	PBDE	blood:	n/a	chr3:19990147-19990157
44	PML	chr3:19987602-19989745	K562	blood:	n/a	chr3:19989187-19989196 chr3:19989190-19989199
45	UBTF	chr3:19987157-19989859	K562	blood:	n/a	n/a
46	MYC	chr3:19986886-19989780	K562	blood:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
47	YY1	chr3:19989024-19989656	HepG2	liver:	n/a	chr3:19989269-19989277 chr3:19989258-19989280
48	ELF1	chr3:19988195-19989610	HCT-116	colon:	n/a	n/a
49	YY1	chr3:19987955-19989592	SK-N-SH_RA	brain:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19987999-19988008 chr3:19988151-19988159 chr3:19989258-19989280
50	GABPA	chr3:19988260-19989541	K562	blood:	n/a	chr3:19988538-19988545

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987782..19990680-chr3:20013275..20017779,4	K562	blood:
3	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
4	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
5	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
6	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
7	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:
8	chr3:19188168..19190474-chr3:19988134..19989911,2	MCF-7	breast:
9	chr14:24899081..24899637-chr3:19988552..19989514,2	Hela-S3	cervix:
10	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

Variant related genes	Relation type
EFHB	TF binding region
RAB5A	TF binding region
HSPA8P18	TF binding region
ENSG00000183960	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000163576	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000144566	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12486406	0.84[ASN][1000 genomes]
rs12489907	0.92[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12496392	0.92[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12496946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13078869	0.88[ASN][1000 genomes]
rs13079277	0.88[ASN][1000 genomes]
rs13098043	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13098054	0.89[ASN][1000 genomes]
rs34050713	0.89[ASN][1000 genomes]
rs34468236	0.88[ASN][1000 genomes]
rs34955379	0.89[ASN][1000 genomes]
rs35094497	0.80[ASN][1000 genomes]
rs35172759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35757621	0.85[ASN][1000 genomes]
rs4241540	1.00[YRI][hapmap]
rs4858660	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6778866	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7625149	0.85[ASN][1000 genomes]
rs8682	0.92[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9968122	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11716116	DAZL	cis	parietal	SCAN
rs11716116	RAB5A	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19986800-19990200	Active TSS	Duodenum Mucosa	Duodenum
2	chr3:19987000-19989600	Active TSS	Liver	Liver
3	chr3:19987200-19989800	Active TSS	Pancreas	Pancrea
4	chr3:19987200-19990400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:19987200-19990400	Active TSS	Placenta	Placenta
6	chr3:19987200-19990600	Active TSS	K562	blood
7	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:19987400-19989800	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr3:19987400-19990000	Active TSS	Brain Germinal Matrix	brain
10	chr3:19987400-19990000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:19987400-19990000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr3:19987400-19990000	Active TSS	A549	lung
13	chr3:19987400-19990200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:19987400-19990200	Active TSS	HSMM	muscle
15	chr3:19987400-19990400	Active TSS	NHDF-Ad	bronchial
16	chr3:19987400-19990800	Active TSS	Right Atrium	heart
17	chr3:19987400-19990800	Active TSS	HSMMtube	muscle
18	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:19987600-19989600	Active TSS	Brain Cingulate Gyrus	brain
20	chr3:19987600-19989800	Active TSS	Brain Hippocampus Middle	brain
21	chr3:19987600-19989800	Active TSS	Left Ventricle	heart
22	chr3:19987600-19989800	Active TSS	Lung	lung
23	chr3:19987600-19990000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:19987600-19990000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:19987600-19990000	Active TSS	Ovary	ovary
26	chr3:19987600-19990000	Active TSS	Thymus	Thymus
27	chr3:19987600-19990200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:19987600-19990200	Active TSS	Colon Smooth Muscle	Colon
29	chr3:19987600-19990400	Active TSS	Colonic Mucosa	Colon
30	chr3:19987600-19990400	Active TSS	Fetal Kidney	kidney
31	chr3:19987600-19990800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr3:19987600-19991000	Active TSS	NHLF	lung
33	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:19987800-19989800	Active TSS	Esophagus	oesophagus
35	chr3:19987800-19989800	Active TSS	Fetal Heart	heart
36	chr3:19987800-19989800	Active TSS	Small Intestine	intestine
37	chr3:19987800-19990000	Active TSS	Aorta	Aorta
38	chr3:19987800-19990000	Active TSS	Fetal Muscle Trunk	muscle
39	chr3:19987800-19990000	Active TSS	Stomach Mucosa	stomach
40	chr3:19987800-19990400	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr3:19987800-19990400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:19987800-19990800	Active TSS	Psoas Muscle	Psoas
43	chr3:19987800-19990800	Active TSS	Right Ventricle	heart
44	chr3:19987800-19991400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr3:19987800-19991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:19988000-19989600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:19988000-19989600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:19988000-19989600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:19988000-19989600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr3:19988000-19989600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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