Variant report

Variant	rs4656727
Chromosome Location	chr1:169862793-169862794
allele	A/G
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	JUND	chr1:169862593-169863706	A549	lung:	n/a	chr1:169863455-169863464 chr1:169863477-169863486
2	POLR2A	chr1:169861889-169863963	GM19099	blood:	n/a	n/a
3	ELF1	chr1:169862511-169863663	K562	blood:	n/a	n/a
4	RFX5	chr1:169861477-169864046	SK-N-SH	brain:	n/a	chr1:169863478-169863487
5	SP2	chr1:169862721-169863692	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:169862498-169862807	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr1:169862421-169863766	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:169862452-169863851	MCF-7	breast:	n/a	n/a
9	EP300	chr1:169862716-169863245	T-47D	breast:	n/a	n/a
10	POLR2A	chr1:169862149-169864267	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOXM1	chr1:169862793-169863490	GM12878	blood:	n/a	n/a
12	MAX	chr1:169862446-169863753	K562	blood:	n/a	n/a
13	REST	chr1:169862780-169863270	HepG2	liver:	n/a	n/a
14	RCOR1	chr1:169862459-169863529	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:169862538-169863227	HCT-116	colon:	n/a	n/a
16	POLR2A	chr1:169862354-169864005	ProgFib	skin:	n/a	n/a
17	SP1	chr1:169862792-169863730	A549	lung:	n/a	chr1:169863468-169863489
18	NFATC1	chr1:169862741-169863230	GM12878	blood:	n/a	n/a
19	TAL1	chr1:169862648-169864025	K562	blood:	n/a	n/a
20	CREB1	chr1:169862356-169863786	HepG2	liver:	n/a	chr1:169863453-169863466
21	EBF1	chr1:169862785-169863241	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:169862470-169864082	SK-N-SH	brain:	n/a	n/a
23	HCFC1	chr1:169861435-169864287	Hela-S3	cervix:	n/a	n/a
24	SMARCB1	chr1:169862319-169863947	Hela-S3	cervix:	n/a	n/a
25	TAF1	chr1:169862491-169863604	H1-neurons	neurons:	n/a	n/a
26	SP1	chr1:169862731-169863617	GM12878	blood:	n/a	chr1:169863468-169863489
27	POLR2A	chr1:169862495-169864014	HEK293	kidney:	n/a	n/a
28	CREB1	chr1:169862480-169863800	GM12878	blood:	n/a	chr1:169863453-169863466
29	MAZ	chr1:169862544-169863819	GM12878	blood:	n/a	n/a
30	CREB1	chr1:169862518-169863961	K562	blood:	n/a	chr1:169863453-169863466
31	POLR2A	chr1:169862376-169863791	Hela-S3	cervix:	n/a	n/a
32	YY1	chr1:169862518-169863592	GM12891	blood:	n/a	chr1:169863368-169863376 chr1:169862643-169862654 chr1:169863190-169863212 chr1:169863357-169863379 chr1:169863369-169863379 chr1:169863189-169863201
33	POLR2A	chr1:169861160-169864335	GM12878	blood:	n/a	n/a
34	ELK1	chr1:169862654-169863892	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:169862090-169863924	Hela-S3	cervix:	n/a	n/a
36	TAF1	chr1:169862629-169863513	GM12878	blood:	n/a	n/a
37	YY1	chr1:169862555-169863656	GM12878	blood:	n/a	chr1:169863368-169863376 chr1:169862643-169862654 chr1:169863190-169863212 chr1:169863357-169863379 chr1:169863369-169863379 chr1:169863189-169863201
38	POLR2A	chr1:169862585-169863115	HepG2	liver:	n/a	n/a
39	RCOR1	chr1:169862627-169863530	GM12878	blood:	n/a	n/a
40	SP4	chr1:169862682-169863496	H1-hESC	embryonic stem cell:	n/a	n/a
41	POU2F2	chr1:169862729-169863370	GM12891	blood:	n/a	n/a
42	POLR2A	chr1:169862539-169863801	MCF-7	breast:	n/a	n/a
43	TBP	chr1:169862119-169863861	K562	blood:	n/a	n/a
44	RELA	chr1:169862602-169863605	GM10847	blood:	n/a	n/a
45	TAF1	chr1:169862441-169863684	GM12878	blood:	n/a	n/a
46	ELF1	chr1:169862573-169863883	HCT-116	colon:	n/a	n/a
47	YY1	chr1:169862547-169863697	A549	lung:	n/a	chr1:169863368-169863376 chr1:169862643-169862654 chr1:169863190-169863212 chr1:169863357-169863379 chr1:169863369-169863379 chr1:169863189-169863201
48	POLR2A	chr1:169862505-169863878	PFSK-1	brain:	n/a	n/a
49	HEY1	chr1:169862536-169863262	HepG2	liver:	n/a	chr1:169862588-169862603
50	MYC	chr1:169862755-169863752	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:6639783..6640313-chr1:169862702..169863370,2	Hela-S3	cervix:
2	chr1:169861326..169864449-chr1:170043806..170046469,4	K562	blood:
3	chr1:169862684..169863338-chr4:146101247..146102153,2	Hela-S3	cervix:
4	chr1:169862487..169863108-chr15:65588179..65588956,2	Hela-S3	cervix:
5	chr1:169862567..169863163-chr17:57183700..57184660,2	Hela-S3	cervix:
6	chr1:169862288..169862861-chr17:7738385..7739270,2	Hela-S3	cervix:
7	chr1:169862596..169865250-chr1:170499667..170504019,5	K562	blood:
8	chr1:169862195..169863184-chr2:70528826..70529358,2	Hela-S3	cervix:
9	chr1:169763198..169765886-chr1:169860155..169862900,4	K562	blood:
10	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
11	chr1:169862420..169863260-chr7:12726780..12727377,2	Hela-S3	cervix:
12	chr1:169862704..169863379-chr17:42580368..42581030,2	Hela-S3	cervix:
13	chr1:169862774..169863319-chr2:102314198..102314758,2	Hela-S3	cervix:
14	chr1:169862763..169864506-chr1:170500944..170502450,2	K562	blood:
15	chr1:169862177..169865166-chr1:170500254..170502788,2	MCF-7	breast:
16	chr1:169763753..169765531-chr1:169862183..169864517,2	MCF-7	breast:
17	chr1:169862695..169863202-chr11:76155222..76156123,2	Hela-S3	cervix:
18	chr1:169862694..169863202-chr5:86563268..86564128,2	Hela-S3	cervix:
19	chr1:169862283..169862808-chr15:41098940..41099495,2	Hela-S3	cervix:
20	chr1:169708422..169710485-chr1:169860930..169862840,2	MCF-7	breast:
21	chr1:169862471..169864194-chr12:53738889..53741815,2	MCF-7	breast:
22	chr1:169845717..169848182-chr1:169860925..169862962,2	MCF-7	breast:
23	chr1:169764521..169766056-chr1:169860447..169863119,2	MCF-7	breast:
24	chr1:169770689..169773107-chr1:169861267..169863060,2	K562	blood:
25	chr1:169770089..169773107-chr1:169860421..169863060,3	K562	blood:
26	chr1:169763198..169765715-chr1:169860443..169862900,3	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000120370	Chromatin interaction
ENSG00000075945	Chromatin interaction
ENSG00000145715	Chromatin interaction
ENSG00000164164	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000158636	Chromatin interaction
ENSG00000255135	Chromatin interaction
ENSG00000204859	Chromatin interaction
ENSG00000231407	Chromatin interaction
ENSG00000122644	Chromatin interaction
ENSG00000035141	Chromatin interaction
ENSG00000170374	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000186566	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000071054	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10800488	0.82[EUR][1000 genomes]
rs11577641	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11579102	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11582552	0.88[EUR][1000 genomes]
rs11585093	0.83[EUR][1000 genomes]
rs35196850	0.85[EUR][1000 genomes]
rs3753312	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3766150	0.84[EUR][1000 genomes]
rs4656201	0.86[EUR][1000 genomes]
rs4656726	0.84[EUR][1000 genomes]
rs55806711	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61806076	0.82[EUR][1000 genomes]
rs61807835	0.86[EUR][1000 genomes]
rs61807840	0.85[EUR][1000 genomes]
rs73026253	0.84[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169861200-169863800	Active TSS	Aorta	Aorta
2	chr1:169861200-169864000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:169861400-169863400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:169861400-169864000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:169861400-169864000	Active TSS	Colonic Mucosa	Colon
6	chr1:169861600-169863800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:169861600-169863800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:169861600-169863800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:169861600-169863800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:169861600-169863800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:169861600-169863800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:169861600-169863800	Active TSS	GM12878-XiMat	blood
13	chr1:169861600-169863800	Active TSS	HSMM	muscle
14	chr1:169861600-169864000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:169861600-169864000	Active TSS	Psoas Muscle	Psoas
16	chr1:169861600-169864000	Active TSS	Right Atrium	heart
17	chr1:169861600-169864000	Active TSS	HSMMtube	muscle
18	chr1:169861800-169863400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:169861800-169863400	Active TSS	Lung	lung
20	chr1:169861800-169863600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:169861800-169863600	Active TSS	NHEK	skin
22	chr1:169861800-169863600	Active TSS	NHLF	lung
23	chr1:169861800-169863800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:169861800-169863800	Active TSS	Fetal Muscle Trunk	muscle
25	chr1:169861800-169863800	Active TSS	Stomach Mucosa	stomach
26	chr1:169861800-169863800	Active TSS	NHDF-Ad	bronchial
27	chr1:169861800-169864000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:169861800-169864000	Active TSS	Esophagus	oesophagus
29	chr1:169861800-169864000	Active TSS	Left Ventricle	heart
30	chr1:169861800-169864000	Active TSS	Placenta Amnion	Placenta Amnion
31	chr1:169861800-169864000	Active TSS	Right Ventricle	heart
32	chr1:169862000-169863400	Active TSS	Gastric	stomach
33	chr1:169862000-169863400	Active TSS	Small Intestine	intestine
34	chr1:169862000-169863600	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr1:169862000-169863600	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr1:169862000-169863600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:169862000-169863600	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr1:169862000-169863600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:169862000-169863600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr1:169862000-169863600	Active TSS	Fetal Intestine Large	intestine
41	chr1:169862000-169863600	Active TSS	Thymus	Thymus
42	chr1:169862000-169863800	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:169862000-169863800	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr1:169862000-169863800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:169862000-169863800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:169862000-169863800	Active TSS	Liver	Liver
47	chr1:169862000-169863800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:169862000-169863800	Active TSS	Brain Substantia Nigra	brain
49	chr1:169862000-169863800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:169862000-169863800	Active TSS	Fetal Intestine Small	intestine

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