Variant report

Variant	rs1200129
Chromosome Location	chr1:169077127-169077128
allele	A/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	CREB1	chr1:169077001-169077346	A549	lung:	n/a	n/a
2	WRNIP1	chr1:169076027-169077144	GM12878	blood:	n/a	n/a
3	FOS	chr1:169077051-169077417	MCF10A-Er-Src	breast:	n/a	chr1:169077258-169077269
4	SIN3AK20	chr1:169074606-169077295	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:169074739-169077862	Hela-S3	cervix:	n/a	n/a
6	TAF1	chr1:169077073-169077280	SK-N-SH	brain:	n/a	n/a
7	RFX5	chr1:169074822-169077754	Hela-S3	cervix:	n/a	chr1:169077634-169077643
8	POLR2A	chr1:169077104-169077187	A549	lung:	n/a	n/a
9	POLR2A	chr1:169074709-169082197	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:169077001-169077266	A549	lung:	n/a	n/a
11	TBP	chr1:169076358-169077243	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr1:169074867-169077276	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:169077028-169077260	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAFK	chr1:169076363-169078735	Hela-S3	cervix:	n/a	n/a
15	MAFF	chr1:169077099-169077407	HepG2	liver:	n/a	n/a
16	MAFK	chr1:169077101-169077460	HepG2	liver:	n/a	n/a
17	TAF1	chr1:169076780-169077320	A549	lung:	n/a	n/a
18	RCOR1	chr1:169076359-169077479	Hela-S3	cervix:	n/a	n/a
19	SMC3	chr1:169074866-169077305	Hela-S3	cervix:	n/a	chr1:169076006-169076016
20	KAP1	chr1:169076043-169077127	HEK293	kidney:	n/a	n/a
21	USF2	chr1:169077079-169077262	Hela-S3	cervix:	n/a	n/a
22	TAF1	chr1:169077019-169077321	Hela-S3	cervix:	n/a	n/a
23	FOS	chr1:169076857-169077438	HUVEC	blood vessel:	n/a	chr1:169077258-169077269
24	POLR2A	chr1:169076380-169077412	Hela-S3	cervix:	n/a	n/a
25	SMARCC1	chr1:169075987-169079359	Hela-S3	cervix:	n/a	n/a
26	FOSL2	chr1:169076339-169077494	A549	lung:	n/a	n/a
27	RAD21	chr1:169076281-169077262	Hela-S3	cervix:	n/a	chr1:169077102-169077114 chr1:169076719-169076731
28	REST	chr1:169076257-169077794	A549	lung:	n/a	chr1:169077629-169077639 chr1:169076262-169076275
29	SP1	chr1:169076865-169077397	A549	lung:	n/a	chr1:169077107-169077121
30	ZNF263	chr1:169074720-169079408	HEK293-T-REx	kidney:	n/a	chr1:169077070-169077079 chr1:169077110-169077119
31	POLR2A	chr1:169077005-169077309	MCF-7	breast:	n/a	n/a
32	POLR2A	chr1:169077002-169077384	Hela-S3	cervix:	n/a	n/a
33	HEY1	chr1:169077031-169077289	HepG2	liver:	n/a	n/a
34	RELA	chr1:169076409-169077249	GM19099	blood:	n/a	n/a
35	CTCF	chr1:169077040-169077195	GM19239	blood:	n/a	n/a
36	RAD21	chr1:169074403-169080488	SK-N-SH	brain:	n/a	chr1:169077102-169077114 chr1:169078627-169078641 chr1:169076719-169076731 chr1:169077792-169077801 chr1:169079920-169079939
37	RAD21	chr1:169075374-169077332	IMR90	lung:	n/a	chr1:169077102-169077114 chr1:169076719-169076731
38	POLR2A	chr1:169075357-169077971	IMR90	lung:	n/a	n/a
39	POLR2A	chr1:169077012-169077330	Hela-S3	cervix:	n/a	n/a
40	BRCA1	chr1:169076914-169077508	Hela-S3	cervix:	n/a	n/a
41	TCF12	chr1:169074352-169077666	A549	lung:	n/a	chr1:169075044-169075054 chr1:169075804-169075811 chr1:169075253-169075260
42	POLR2A	chr1:169077015-169077232	A549	lung:	n/a	n/a
43	REST	chr1:169074554-169080074	H1-neurons	neurons:	n/a	chr1:169075463-169075476 chr1:169077629-169077639 chr1:169078558-169078578 chr1:169076262-169076275 chr1:169076181-169076191 chr1:169075295-169075305 chr1:169075034-169075047 chr1:169075245-169075258
44	POLR2A	chr1:169074699-169077343	GM18951	blood:	n/a	n/a
45	MAX	chr1:169074863-169077471	Hela-S3	cervix:	n/a	chr1:169075667-169075677 chr1:169076272-169076282 chr1:169075347-169075357 chr1:169077106-169077116
46	POLR2A	chr1:169077009-169077270	A549	lung:	n/a	n/a
47	MYC	chr1:169077035-169077158	MCF-7	breast:	n/a	chr1:169077106-169077116
48	RFX5	chr1:169074571-169080541	SK-N-SH	brain:	n/a	chr1:169077634-169077643
49	POLR2A	chr1:169077017-169077259	A549	lung:	n/a	n/a
50	ZNF384	chr1:169076872-169077199	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:168907357..168910687-chr1:169076812..169079423,3	MCF-7	breast:
2	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
3	chr1:169053133..169065213-chr1:169070028..169077898,15	MCF-7	breast:
4	chr1:168865232..168870287-chr1:169075405..169077247,5	MCF-7	breast:
5	chr1:169075479..169078672-chr1:169335264..169338570,4	MCF-7	breast:

Variant related genes	Relation type
ATP1B1	TF binding region
ENSG00000203601	Chromatin interaction
ENSG00000143156	Chromatin interaction
ENSG00000229612	Chromatin interaction
ENSG00000117475	Chromatin interaction
ENSG00000213063	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1200116	0.84[EUR][1000 genomes]
rs28362571	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169074000-169078800	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:169074400-169077400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:169074600-169077600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr1:169074600-169077800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:169074600-169077800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:169074600-169078000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:169074800-169077200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:169074800-169077200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:169074800-169077200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:169074800-169077200	Active TSS	Duodenum Mucosa	Duodenum
11	chr1:169074800-169077400	Active TSS	Brain Germinal Matrix	brain
12	chr1:169074800-169077600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:169074800-169078000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:169074800-169078000	Active TSS	Ovary	ovary
15	chr1:169074800-169078000	Active TSS	Psoas Muscle	Psoas
16	chr1:169074800-169078200	Active TSS	Small Intestine	intestine
17	chr1:169074800-169078800	Active TSS	Brain Substantia Nigra	brain
18	chr1:169074800-169079000	Active TSS	Fetal Kidney	kidney
19	chr1:169074800-169079200	Active TSS	Brain Hippocampus Middle	brain
20	chr1:169074800-169079400	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr1:169074800-169079600	Active TSS	Stomach Mucosa	stomach
22	chr1:169074800-169079800	Active TSS	Left Ventricle	heart
23	chr1:169074800-169080400	Active TSS	Right Ventricle	heart
24	chr1:169074800-169080800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr1:169075000-169077200	Active TSS	Aorta	Aorta
26	chr1:169075000-169077400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:169075000-169077400	Active TSS	Hela-S3	cervix
28	chr1:169075000-169077400	Active TSS	NHLF	lung
29	chr1:169075000-169077600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr1:169075000-169077600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:169075000-169077600	Active TSS	Pancreas	Pancrea
32	chr1:169075000-169077800	Active TSS	Fetal Brain Female	brain
33	chr1:169075000-169078000	Active TSS	Fetal Intestine Small	intestine
34	chr1:169075000-169078000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:169075000-169079200	Active TSS	Esophagus	oesophagus
36	chr1:169075000-169079200	Active TSS	Fetal Intestine Large	intestine
37	chr1:169075000-169079200	Active TSS	Gastric	stomach
38	chr1:169075000-169079400	Active TSS	Colon Smooth Muscle	Colon
39	chr1:169075000-169080000	Active TSS	Brain Anterior Caudate	brain
40	chr1:169075000-169080000	Active TSS	GM12878-XiMat	blood
41	chr1:169075000-169080400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:169075000-169080600	Active TSS	Brain Cingulate Gyrus	brain
43	chr1:169075200-169077200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr1:169075200-169077400	Active TSS	Fetal Muscle Trunk	muscle
45	chr1:169075200-169077400	Active TSS	Stomach Smooth Muscle	stomach
46	chr1:169075200-169077400	Active TSS	HMEC	breast
47	chr1:169075200-169077600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:169075200-169077600	Active TSS	Placenta Amnion	Placenta Amnion
49	chr1:169075200-169077600	Active TSS	Thymus	Thymus
50	chr1:169075200-169077800	Active TSS	Lung	lung

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