Variant report

Variant	rs12077708
Chromosome Location	chr1:169861638-169861639
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	RFX5	chr1:169861477-169864046	SK-N-SH	brain:	n/a	chr1:169863478-169863487
2	MAFF	chr1:169861436-169862092	HepG2	liver:	n/a	chr1:169861777-169861795
3	HCFC1	chr1:169861435-169864287	Hela-S3	cervix:	n/a	n/a
4	MAFK	chr1:169861561-169862264	K562	blood:	n/a	chr1:169861780-169861791 chr1:169861778-169861792 chr1:169861780-169861791 chr1:169861779-169861790 chr1:169861573-169861593 chr1:169861779-169861794 chr1:169861779-169861790
5	POLR2A	chr1:169861160-169864335	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:169861371-169863975	GM12878	blood:	n/a	n/a
7	MAFK	chr1:169861412-169862059	HepG2	liver:	n/a	chr1:169861780-169861791 chr1:169861778-169861792 chr1:169861780-169861791 chr1:169861779-169861790 chr1:169861573-169861593 chr1:169861779-169861794 chr1:169861779-169861790
8	MAFK	chr1:169861531-169862095	IMR90	lung:	n/a	chr1:169861780-169861791 chr1:169861778-169861792 chr1:169861780-169861791 chr1:169861779-169861790 chr1:169861573-169861593 chr1:169861779-169861794 chr1:169861779-169861790
9	JUND	chr1:169861502-169864054	SK-N-SH	brain:	n/a	chr1:169863455-169863464 chr1:169863477-169863486
10	MAFK	chr1:169861432-169862272	Hela-S3	cervix:	n/a	chr1:169861780-169861791 chr1:169861778-169861792 chr1:169861780-169861791 chr1:169861779-169861790 chr1:169861573-169861593 chr1:169861779-169861794 chr1:169861779-169861790
11	POLR2A	chr1:169861628-169864110	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:169861236-169864286	GM12891	blood:	n/a	n/a
13	MAFK	chr1:169861391-169862597	GM12878	blood:	n/a	chr1:169861780-169861791 chr1:169861778-169861792 chr1:169861780-169861791 chr1:169861779-169861790 chr1:169861573-169861593 chr1:169861779-169861794 chr1:169861779-169861790
14	MAFF	chr1:169861597-169862239	K562	blood:	n/a	chr1:169861777-169861795
15	MTA3	chr1:169861548-169862421	GM12878	blood:	n/a	n/a
16	MAFK	chr1:169861462-169862054	HepG2	liver:	n/a	chr1:169861780-169861791 chr1:169861778-169861792 chr1:169861780-169861791 chr1:169861779-169861790 chr1:169861573-169861593 chr1:169861779-169861794 chr1:169861779-169861790
17	MAFK	chr1:169861573-169861975	H1-hESC	embryonic stem cell:	n/a	chr1:169861780-169861791 chr1:169861778-169861792 chr1:169861780-169861791 chr1:169861779-169861790 chr1:169861573-169861593 chr1:169861779-169861794 chr1:169861779-169861790
18	STAT1	chr1:169861495-169863919	Hela-S3	cervix:	n/a	chr1:169862349-169862360 chr1:169863112-169863120

No.	Distal block	Cell Line	Cell type
1	chr1:169861326..169864449-chr1:170043806..170046469,4	K562	blood:
2	chr1:169704931..169706505-chr1:169859799..169862220,2	K562	blood:
3	chr1:169763198..169765886-chr1:169860155..169862900,4	K562	blood:
4	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
5	chr1:169708422..169710485-chr1:169860930..169862840,2	MCF-7	breast:
6	chr1:169845717..169848182-chr1:169860925..169862962,2	MCF-7	breast:
7	chr1:169764521..169766056-chr1:169860447..169863119,2	MCF-7	breast:
8	chr1:169770689..169773107-chr1:169861267..169863060,2	K562	blood:
9	chr1:169770089..169773107-chr1:169860421..169863060,3	K562	blood:
10	chr1:169763198..169765715-chr1:169860443..169862900,3	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000075945	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10458398	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800487	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10919268	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919269	1.00[ASN][1000 genomes]
rs10919276	1.00[EUR][1000 genomes]
rs10919288	1.00[EUR][1000 genomes]
rs10919294	1.00[EUR][1000 genomes]
rs10919295	1.00[EUR][1000 genomes]
rs10919296	1.00[EUR][1000 genomes]
rs10919300	1.00[EUR][1000 genomes]
rs12023729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12024570	1.00[ASN][1000 genomes]
rs12025296	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027790	1.00[ASN][1000 genomes]
rs12032210	0.82[CHB][hapmap]
rs12035711	1.00[ASN][1000 genomes]
rs12044536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066551	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071325	1.00[EUR][1000 genomes]
rs12076018	1.00[EUR][1000 genomes]
rs12079608	1.00[EUR][1000 genomes]
rs12083317	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12090220	1.00[EUR][1000 genomes]
rs12095784	1.00[EUR][1000 genomes]
rs13374781	1.00[EUR][1000 genomes]
rs13375701	1.00[EUR][1000 genomes]
rs16862886	1.00[EUR][1000 genomes]
rs16862978	1.00[EUR][1000 genomes]
rs2103641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272912	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272915	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2901261	1.00[EUR][1000 genomes]
rs3790406	1.00[JPT][hapmap]
rs4279900	1.00[EUR][1000 genomes]
rs56084868	1.00[EUR][1000 genomes]
rs57038529	1.00[EUR][1000 genomes]
rs73041439	1.00[EUR][1000 genomes]
rs74121797	1.00[EUR][1000 genomes]
rs74122312	1.00[EUR][1000 genomes]
rs74122421	1.00[EUR][1000 genomes]
rs74122422	1.00[EUR][1000 genomes]
rs74122452	1.00[EUR][1000 genomes]
rs7531947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532990	1.00[ASN][1000 genomes]
rs7533350	1.00[ASN][1000 genomes]
rs989054	1.00[EUR][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169852600-169862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:169859000-169861800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:169859000-169861800	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr1:169859400-169862000	Weak transcription	Ovary	ovary
6	chr1:169860000-169861800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:169860000-169861800	Enhancers	Placenta	Placenta
8	chr1:169860000-169861800	Enhancers	Stomach Mucosa	stomach
9	chr1:169860000-169862000	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:169860000-169862000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr1:169860000-169862000	Flanking Active TSS	A549	lung
12	chr1:169860000-169862200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:169860000-169862200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:169860000-169862200	Enhancers	Spleen	Spleen
15	chr1:169860000-169862400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:169860200-169861800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr1:169860400-169861800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:169860400-169862000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:169860400-169862200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:169860600-169861800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:169860600-169861800	Enhancers	Primary B cells from cord blood	blood
22	chr1:169860600-169861800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:169860600-169861800	Enhancers	Fetal Heart	heart
24	chr1:169860600-169862000	Weak transcription	Pancreas	Pancrea
25	chr1:169860800-169861800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:169860800-169861800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:169860800-169861800	Enhancers	Fetal Muscle Leg	muscle
28	chr1:169861000-169861800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:169861200-169861800	Flanking Active TSS	NHEK	skin
30	chr1:169861200-169862000	Flanking Active TSS	Liver	Liver
31	chr1:169861200-169862000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:169861200-169862000	Flanking Active TSS	HepG2	liver
33	chr1:169861200-169862200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr1:169861200-169863800	Active TSS	Aorta	Aorta
35	chr1:169861200-169864000	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr1:169861400-169861800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:169861400-169861800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:169861400-169861800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:169861400-169861800	Enhancers	Esophagus	oesophagus
40	chr1:169861400-169861800	Enhancers	Fetal Brain Male	brain
41	chr1:169861400-169861800	Enhancers	Left Ventricle	heart
42	chr1:169861400-169861800	Enhancers	Lung	lung
43	chr1:169861400-169861800	Enhancers	Right Ventricle	heart
44	chr1:169861400-169861800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr1:169861400-169862000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:169861400-169862000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:169861400-169862000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:169861400-169862000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:169861400-169862000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:169861400-169862000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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