Variant report

Variant	rs61739366
Chromosome Location	chr9:100395819-100395820
allele	C/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	WRNIP1	chr9:100394487-100396215	GM12878	blood:	n/a	n/a
2	BCLAF1	chr9:100395021-100396733	GM12878	blood:	n/a	chr9:100396673-100396682 chr9:100395612-100395621 chr9:100396377-100396386 chr9:100396312-100396321
3	SP2	chr9:100395496-100396136	K562	blood:	n/a	n/a
4	SIN3AK20	chr9:100394910-100396672	H1-hESC	embryonic stem cell:	n/a	n/a
5	CREB1	chr9:100394800-100396063	ECC-1	luminal epithelium:	n/a	chr9:100395644-100395657
6	JUND	chr9:100394926-100395972	HepG2	liver:	n/a	chr9:100395646-100395655 chr9:100395491-100395505
7	ARID3A	chr9:100394817-100396132	HepG2	liver:	n/a	n/a
8	PBX3	chr9:100395719-100395886	GM12878	blood:	n/a	n/a
9	STAT3	chr9:100394934-100395908	MCF10A-Er-Src	breast:	n/a	n/a
10	YY1	chr9:100395700-100396188	GM12891	blood:	n/a	n/a
11	POLR2A	chr9:100394955-100396311	HCT-116	colon:	n/a	n/a
12	FOS	chr9:100394910-100396065	HUVEC	blood vessel:	n/a	chr9:100395646-100395655 chr9:100395491-100395505
13	TRIM28	chr9:100394916-100395889	K562	blood:	n/a	n/a
14	EP300	chr9:100395636-100396272	A549	lung:	n/a	chr9:100396213-100396229 chr9:100395915-100395931 chr9:100395773-100395782 chr9:100395662-100395669
15	POLR2A	chr9:100394061-100396885	MCF10A-Er-Src	breast:	n/a	n/a
16	MAX	chr9:100395000-100396292	K562	blood:	n/a	n/a
17	TCF12	chr9:100394697-100396492	A549	lung:	n/a	chr9:100395316-100395325
18	IRF1	chr9:100394552-100396284	K562	blood:	n/a	chr9:100395412-100395426 chr9:100395430-100395444 chr9:100395551-100395560
19	TBP	chr9:100394943-100396329	GM12878	blood:	n/a	n/a
20	ZNF143	chr9:100395112-100396180	H1-hESC	embryonic stem cell:	n/a	chr9:100395434-100395453
21	BHLHE40	chr9:100394719-100396515	K562	blood:	n/a	chr9:100395405-100395414 chr9:100395405-100395414
22	GABPA	chr9:100395297-100396247	HepG2	liver:	n/a	n/a
23	CHD2	chr9:100395124-100396291	Hela-S3	cervix:	n/a	chr9:100395419-100395429
24	EP300	chr9:100395251-100396215	H1-hESC	embryonic stem cell:	n/a	chr9:100395315-100395325 chr9:100395915-100395931 chr9:100395773-100395782 chr9:100395662-100395669
25	POLR2A	chr9:100394139-100396624	HepG2	liver:	n/a	n/a
26	TAF1	chr9:100395213-100396374	HepG2	liver:	n/a	n/a
27	CBX3	chr9:100395739-100396222	K562	blood:	n/a	n/a
28	TAF1	chr9:100394972-100396517	ECC-1	luminal epithelium:	n/a	n/a
29	SRF	chr9:100395349-100396106	ECC-1	luminal epithelium:	n/a	n/a
30	FOXP2	chr9:100395554-100396144	SK-N-MC	brain:	n/a	n/a
31	JUN	chr9:100394881-100396232	K562	blood:	n/a	chr9:100395646-100395655 chr9:100395115-100395128 chr9:100395491-100395505
32	POLR2A	chr9:100395788-100396250	GM12891	blood:	n/a	n/a
33	CTCF	chr9:100395800-100395950	HepG2	liver:	n/a	chr9:100395918-100395931
34	TBL1XR1	chr9:100395153-100396156	K562	blood:	n/a	n/a
35	CTCF	chr9:100395740-100395890	GM12865	blood:	n/a	n/a
36	GABPA	chr9:100395365-100396217	K562	blood:	n/a	n/a
37	POLR2A	chr9:100395105-100396331	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:100394453-100396602	H1-hESC	embryonic stem cell:	n/a	n/a
39	ELK4	chr9:100395482-100396054	HEK293	kidney:	n/a	chr9:100395660-100395671
40	MYC	chr9:100394957-100396243	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr9:100395800-100395950	NHDF-neo	bronchial:	n/a	chr9:100395918-100395931
42	POLR2A	chr9:100394713-100396337	K562	blood:	n/a	n/a
43	MXI1	chr9:100394848-100396250	K562	blood:	n/a	n/a
44	NRF1	chr9:100395674-100396206	H1-hESC	embryonic stem cell:	n/a	n/a
45	GABPA	chr9:100395335-100396238	HepG2	liver:	n/a	n/a
46	NFYA	chr9:100395528-100396098	Hela-S3	cervix:	n/a	n/a
47	CEBPB	chr9:100394966-100396015	A549	lung:	n/a	n/a
48	ELK1	chr9:100394914-100396190	Hela-S3	cervix:	n/a	n/a
49	PAX5	chr9:100395221-100396364	GM12878	blood:	n/a	chr9:100395550-100395559
50	POU2F2	chr9:100395744-100396195	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:3332578..3333236-chr9:100395488..100396139,2	HCT-116	colon:
2	chr19:18391959..18392574-chr9:100395508..100396344,3	Hela-S3	cervix:
3	chr9:100393858..100397326-chr9:100457081..100460285,5	MCF-7	breast:
4	chr17:62657981..62658934-chr9:100395545..100396374,2	NB4	blood:
5	chr9:100394431..100399065-chr9:100743200..100747046,6	K562	blood:
6	chr9:100393846..100397319-chr9:100457855..100461087,4	MCF-7	breast:
7	chr9:100378318..100380462-chr9:100395388..100397113,2	K562	blood:
8	chr1:16839110..16841676-chr9:100394541..100396656,2	MCF-7	breast:
9	chr9:100395301..100398247-chr9:100745097..100747092,2	MCF-7	breast:
10	chr9:100394343..100396600-chr9:100677965..100680117,2	MCF-7	breast:
11	chr9:100172589..100175955-chr9:100393372..100395869,4	K562	blood:
12	chr9:100364434..100366925-chr9:100393876..100396589,2	MCF-7	breast:
13	chr9:100172235..100177344-chr9:100393372..100396960,5	K562	blood:
14	chr9:100379940..100382784-chr9:100394672..100397527,3	MCF-7	breast:
15	chr1:28974912..28975848-chr9:100395311..100396221,2	Hela-S3	cervix:
16	chr17:80374866..80376675-chr9:100395383..100397394,2	MCF-7	breast:
17	chr9:100279156..100280709-chr9:100395787..100397430,2	K562	blood:
18	chr9:100228650..100231026-chr9:100395241..100396818,2	K562	blood:
19	chr9:100393798..100396909-chr9:100744219..100748139,5	MCF-7	breast:
20	chr9:100263644..100266244-chr9:100394289..100397266,4	K562	blood:
21	chr9:100127196..100129265-chr9:100394272..100396018,2	MCF-7	breast:
22	chr9:100393929..100396893-chr9:100683273..100687162,3	K562	blood:

Variant related genes	Relation type
NCBP1	TF binding region
TSTD2	TF binding region
ENSG00000206652	Chromatin interaction
ENSG00000108854	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000201239	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000136936	Chromatin interaction
ENSG00000136925	Chromatin interaction
ENSG00000196116	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000197816	Chromatin interaction
ENSG00000228174	Chromatin interaction
ENSG00000181396	Chromatin interaction
ENSG00000136842	Chromatin interaction
ENSG00000201830	Chromatin interaction
ENSG00000006194	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000169660	Chromatin interaction
ENSG00000261135	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1034098	0.85[AFR][1000 genomes]
rs1116208	0.85[AFR][1000 genomes]
rs14066	0.85[AFR][1000 genomes]
rs1411344	0.85[AFR][1000 genomes]
rs1543636	0.86[AFR][1000 genomes]
rs16923033	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16923041	0.83[AFR][1000 genomes]
rs1813875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1928641	0.85[AFR][1000 genomes]
rs1928642	0.85[AFR][1000 genomes]
rs2282066	0.84[AFR][1000 genomes]
rs2282067	0.86[AFR][1000 genomes]
rs28403588	0.84[AFR][1000 genomes]
rs28403589	0.85[AFR][1000 genomes]
rs3176635	0.90[AFR][1000 genomes]
rs3176657	0.87[AFR][1000 genomes]
rs3176687	0.91[AFR][1000 genomes]
rs3176706	0.91[AFR][1000 genomes]
rs3176711	0.91[AFR][1000 genomes]
rs3176712	0.91[AFR][1000 genomes]
rs3750370	0.85[AFR][1000 genomes]
rs3802472	0.85[AFR][1000 genomes]
rs3802473	0.85[AFR][1000 genomes]
rs3802474	0.82[AFR][1000 genomes]
rs41274252	0.85[AFR][1000 genomes]
rs55966848	0.86[AFR][1000 genomes]
rs56060429	0.86[AFR][1000 genomes]
rs58146508	0.83[AFR][1000 genomes]
rs58387091	0.85[AFR][1000 genomes]
rs58390229	0.82[AFR][1000 genomes]
rs58637778	0.86[AFR][1000 genomes]
rs58878935	0.85[AFR][1000 genomes]
rs59478543	0.83[AFR][1000 genomes]
rs59662386	0.83[AFR][1000 genomes]
rs59791764	0.86[AFR][1000 genomes]
rs59992945	0.85[AFR][1000 genomes]
rs60026475	0.86[AFR][1000 genomes]
rs60028882	0.85[AFR][1000 genomes]
rs60055057	0.83[AFR][1000 genomes]
rs60596698	0.85[AFR][1000 genomes]
rs60653177	0.85[AFR][1000 genomes]
rs61221847	0.83[AFR][1000 genomes]
rs61276200	0.86[AFR][1000 genomes]
rs61445476	0.86[AFR][1000 genomes]
rs6478304	0.85[AFR][1000 genomes]
rs6478305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7018546	0.86[AFR][1000 genomes]
rs7021377	0.91[AFR][1000 genomes]
rs7025403	0.85[AFR][1000 genomes]
rs7036604	0.84[AFR][1000 genomes]
rs7049183	0.86[AFR][1000 genomes]
rs7341850	0.83[AFR][1000 genomes]
rs73498323	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498324	0.85[AFR][1000 genomes]
rs73498329	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498332	0.83[AFR][1000 genomes]
rs73498338	0.83[AFR][1000 genomes]
rs73498347	0.83[AFR][1000 genomes]
rs73498348	0.83[AFR][1000 genomes]
rs73498355	0.83[AFR][1000 genomes]
rs73498358	0.83[AFR][1000 genomes]
rs73498359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498362	0.83[AFR][1000 genomes]
rs73498365	0.91[AFR][1000 genomes]
rs73500307	0.90[AFR][1000 genomes]
rs73500321	0.91[AFR][1000 genomes]
rs73500392	0.88[AFR][1000 genomes]
rs73502208	0.87[AFR][1000 genomes]
rs73502210	0.87[AFR][1000 genomes]
rs73551090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73552520	0.83[AFR][1000 genomes]
rs73554631	0.83[AFR][1000 genomes]
rs73554641	0.85[AFR][1000 genomes]
rs73554646	0.85[AFR][1000 genomes]
rs73554650	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73554652	0.85[AFR][1000 genomes]
rs7856316	0.85[AFR][1000 genomes]
rs7857174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7859684	0.85[AFR][1000 genomes]
rs7859979	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7866961	0.83[AFR][1000 genomes]
rs7867046	0.85[AFR][1000 genomes]
rs7869683	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 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	chr9:100393800-100397200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:100394000-100396600	Active TSS	Stomach Smooth Muscle	stomach
3	chr9:100394000-100397000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr9:100394000-100397200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr9:100394000-100397600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:100394000-100397600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:100394200-100396000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:100394200-100397200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:100394200-100397200	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr9:100394200-100397200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:100394200-100397200	Active TSS	Colonic Mucosa	Colon
12	chr9:100394200-100397800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr9:100394200-100398600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr9:100394400-100396000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:100394400-100396800	Active TSS	Aorta	Aorta
16	chr9:100394400-100396800	Active TSS	Placenta Amnion	Placenta Amnion
17	chr9:100394400-100396800	Bivalent/Poised TSS	HepG2	liver
18	chr9:100394400-100397000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr9:100394400-100397000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:100394400-100397000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:100394400-100397000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:100394400-100397000	Active TSS	Esophagus	oesophagus
23	chr9:100394400-100397000	Active TSS	Pancreas	Pancrea
24	chr9:100394400-100397000	Active TSS	Stomach Mucosa	stomach
25	chr9:100394400-100397200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:100394400-100397200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:100394400-100397200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:100394400-100397200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:100394400-100397200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:100394400-100397200	Active TSS	Fetal Muscle Trunk	muscle
31	chr9:100394400-100397200	Active TSS	NHDF-Ad	bronchial
32	chr9:100394400-100397400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:100394400-100397600	Active TSS	Psoas Muscle	Psoas
34	chr9:100394400-100398000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:100394400-100399200	Active TSS	Right Atrium	heart
36	chr9:100394600-100396400	Active TSS	Rectal Smooth Muscle	rectum
37	chr9:100394600-100396600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:100394600-100396600	Active TSS	Colon Smooth Muscle	Colon
39	chr9:100394600-100396600	Active TSS	Fetal Kidney	kidney
40	chr9:100394600-100396600	Active TSS	Fetal Stomach	stomach
41	chr9:100394600-100396800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:100394600-100396800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr9:100394600-100396800	Active TSS	Lung	lung
44	chr9:100394600-100396800	Active TSS	HMEC	breast
45	chr9:100394600-100397000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr9:100394600-100397000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr9:100394600-100397000	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr9:100394600-100397000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:100394600-100397000	Active TSS	Ovary	ovary
50	chr9:100394600-100397200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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