Variant report

Variant	rs61326145
Chromosome Location	chr1:169862332-169862333
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	POLR2A	chr1:169861889-169863963	GM19099	blood:	n/a	n/a
2	RFX5	chr1:169861477-169864046	SK-N-SH	brain:	n/a	chr1:169863478-169863487
3	POLR2A	chr1:169862149-169864267	H1-hESC	embryonic stem cell:	n/a	n/a
4	HCFC1	chr1:169861435-169864287	Hela-S3	cervix:	n/a	n/a
5	SMARCB1	chr1:169862319-169863947	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:169861160-169864335	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:169862090-169863924	Hela-S3	cervix:	n/a	n/a
8	TBP	chr1:169862119-169863861	K562	blood:	n/a	n/a
9	POLR2A	chr1:169861987-169864125	K562	blood:	n/a	n/a
10	POLR2A	chr1:169861878-169863661	IMR90	lung:	n/a	n/a
11	POLR2A	chr1:169861371-169863975	GM12878	blood:	n/a	n/a
12	HA-E2F1	chr1:169862259-169863886	MCF-7	breast:	n/a	chr1:169862473-169862482 chr1:169863454-169863463 chr1:169863479-169863488 chr1:169863456-169863465
13	SIN3AK20	chr1:169861960-169862699	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr1:169862282-169863286	K562	blood:	n/a	n/a
15	POLR2A	chr1:169862325-169863753	GM10847	blood:	n/a	n/a
16	POLR2A	chr1:169862214-169863840	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:169861661-169863983	GM19193	blood:	n/a	n/a
18	MTA3	chr1:169861771-169862469	GM12878	blood:	n/a	n/a
19	STAT3	chr1:169862129-169862460	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr1:169861710-169864097	PFSK-1	brain:	n/a	n/a
21	STAT3	chr1:169862253-169862356	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr1:169862318-169864203	SK-N-MC	brain:	n/a	n/a
23	SIN3AK20	chr1:169862322-169863307	K562	blood:	n/a	n/a
24	MAZ	chr1:169861855-169863996	IMR90	lung:	n/a	n/a
25	TBL1XR1	chr1:169862076-169863785	GM12878	blood:	n/a	n/a
26	SIN3A	chr1:169862143-169863576	H1-hESC	embryonic stem cell:	n/a	chr1:169863404-169863415
27	MXI1	chr1:169861926-169863714	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:169861783-169864324	MCF10A-Er-Src	breast:	n/a	n/a
29	CCNT2	chr1:169862301-169863336	K562	blood:	n/a	n/a
30	IRF1	chr1:169861748-169862368	K562	blood:	n/a	n/a
31	MAX	chr1:169862315-169863905	A549	lung:	n/a	n/a
32	POLR2A	chr1:169861810-169863762	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:169862034-169864384	Raji	blood:	n/a	n/a
34	E2F4	chr1:169862326-169863761	K562	blood:	n/a	chr1:169862473-169862482 chr1:169863454-169863463 chr1:169863479-169863488 chr1:169863350-169863365 chr1:169863456-169863465
35	JUND	chr1:169861502-169864054	SK-N-SH	brain:	n/a	chr1:169863455-169863464 chr1:169863477-169863486
36	POLR2A	chr1:169861948-169863760	HepG2	liver:	n/a	n/a
37	JUN	chr1:169861838-169865596	K562	blood:	n/a	chr1:169863455-169863464 chr1:169863451-169863464 chr1:169863477-169863486
38	RCOR1	chr1:169861858-169863969	K562	blood:	n/a	n/a
39	MXI1	chr1:169862236-169863614	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:169862319-169863328	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:169862257-169863877	PBDE	blood:	n/a	n/a
42	SIN3AK20	chr1:169862242-169862524	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMARCC1	chr1:169861907-169863914	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:169861947-169863806	GM12892	blood:	n/a	n/a
45	POLR2A	chr1:169861996-169863930	GM18505	blood:	n/a	n/a
46	MYC	chr1:169862253-169863841	NB4	blood:	n/a	n/a
47	HMGN3	chr1:169862325-169863145	K562	blood:	n/a	n/a
48	POLR2A	chr1:169861628-169864110	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:169861236-169864286	GM12891	blood:	n/a	n/a
50	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

No.	Distal block	Cell Line	Cell type
1	chr1:169861326..169864449-chr1:170043806..170046469,4	K562	blood:
2	chr1:169862288..169862861-chr17:7738385..7739270,2	Hela-S3	cervix:
3	chr1:169862195..169863184-chr2:70528826..70529358,2	Hela-S3	cervix:
4	chr1:169763198..169765886-chr1:169860155..169862900,4	K562	blood:
5	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
6	chr1:169862177..169865166-chr1:170500254..170502788,2	MCF-7	breast:
7	chr1:169763753..169765531-chr1:169862183..169864517,2	MCF-7	breast:
8	chr1:169862283..169862808-chr15:41098940..41099495,2	Hela-S3	cervix:
9	chr1:169708422..169710485-chr1:169860930..169862840,2	MCF-7	breast:
10	chr1:169845717..169848182-chr1:169860925..169862962,2	MCF-7	breast:
11	chr1:169764521..169766056-chr1:169860447..169863119,2	MCF-7	breast:
12	chr1:169770689..169773107-chr1:169861267..169863060,2	K562	blood:
13	chr1:169770089..169773107-chr1:169860421..169863060,3	K562	blood:
14	chr1:169763198..169765715-chr1:169860443..169862900,3	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000171806	Chromatin interaction
ENSG00000231407	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000120370	Chromatin interaction
ENSG00000075945	Chromatin interaction
ENSG00000035141	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12131357	0.95[AFR][1000 genomes]
rs74122418	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74122419	0.94[AFR][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	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169860000-169862400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:169861200-169863800	Active TSS	Aorta	Aorta
4	chr1:169861200-169864000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:169861400-169862400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:169861400-169862400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:169861400-169862400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr1:169861400-169862400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr1:169861400-169862400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:169861400-169862400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr1:169861400-169862400	Flanking Active TSS	Dnd41	blood
12	chr1:169861400-169863400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:169861400-169864000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:169861400-169864000	Active TSS	Colonic Mucosa	Colon
15	chr1:169861600-169862400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr1:169861600-169862400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr1:169861600-169862400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:169861600-169862600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:169861600-169863800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:169861600-169863800	Active TSS	H1 Cell Line	embryonic stem cell
21	chr1:169861600-169863800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:169861600-169863800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:169861600-169863800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:169861600-169863800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:169861600-169863800	Active TSS	GM12878-XiMat	blood
26	chr1:169861600-169863800	Active TSS	HSMM	muscle
27	chr1:169861600-169864000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:169861600-169864000	Active TSS	Psoas Muscle	Psoas
29	chr1:169861600-169864000	Active TSS	Right Atrium	heart
30	chr1:169861600-169864000	Active TSS	HSMMtube	muscle
31	chr1:169861800-169862400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr1:169861800-169862400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:169861800-169862600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr1:169861800-169863400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:169861800-169863400	Active TSS	Lung	lung
36	chr1:169861800-169863600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:169861800-169863600	Active TSS	NHEK	skin
38	chr1:169861800-169863600	Active TSS	NHLF	lung
39	chr1:169861800-169863800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:169861800-169863800	Active TSS	Fetal Muscle Trunk	muscle
41	chr1:169861800-169863800	Active TSS	Stomach Mucosa	stomach
42	chr1:169861800-169863800	Active TSS	NHDF-Ad	bronchial
43	chr1:169861800-169864000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr1:169861800-169864000	Active TSS	Esophagus	oesophagus
45	chr1:169861800-169864000	Active TSS	Left Ventricle	heart
46	chr1:169861800-169864000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr1:169861800-169864000	Active TSS	Right Ventricle	heart
48	chr1:169862000-169862400	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr1:169862000-169862400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:169862000-169862400	Bivalent/Poised TSS	HepG2	liver

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