Variant report

Variant	rs1077919
Chromosome Location	chr6:20213334-20213335
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	SIN3AK20	chr6:20211119-20213474	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:20212454-20213358	K562	blood:	n/a	n/a
3	CHD2	chr6:20212313-20213386	H1-hESC	embryonic stem cell:	n/a	chr6:20212928-20212935 chr6:20213019-20213029
4	POLR2A	chr6:20212091-20213463	Hela-S3	cervix:	n/a	n/a
5	STAT1	chr6:20211329-20213923	Hela-S3	cervix:	n/a	chr6:20212788-20212796 chr6:20213017-20213029 chr6:20213021-20213033
6	POLR2A	chr6:20212172-20214057	K562	blood:	n/a	n/a
7	CHD2	chr6:20211489-20213339	Hela-S3	cervix:	n/a	chr6:20212928-20212935 chr6:20213019-20213029
8	MAX	chr6:20212148-20213725	GM12878	blood:	n/a	chr6:20213566-20213576 chr6:20213556-20213567 chr6:20213555-20213568 chr6:20212961-20212971 chr6:20213557-20213566 chr6:20213490-20213499
9	HEY1	chr6:20212170-20213441	K562	blood:	n/a	chr6:20212825-20212840
10	POLR2A	chr6:20212105-20213452	GM12892	blood:	n/a	n/a
11	POLR2A	chr6:20212387-20213416	HUVEC	blood vessel:	n/a	n/a
12	PML	chr6:20211970-20213480	GM12878	blood:	n/a	chr6:20213099-20213107
13	POLR2A	chr6:20212386-20213708	PANC-1	pancreas:	n/a	n/a
14	TAF1	chr6:20212508-20213347	K562	blood:	n/a	n/a
15	ELF1	chr6:20212180-20213419	GM12878	blood:	n/a	chr6:20212894-20212903
16	ELF1	chr6:20212399-20213391	K562	blood:	n/a	chr6:20212894-20212903
17	POLR2A	chr6:20211253-20213604	GM19193	blood:	n/a	n/a
18	TBL1XR1	chr6:20212601-20213339	K562	blood:	n/a	n/a
19	BRCA1	chr6:20212673-20213405	Hela-S3	cervix:	n/a	n/a
20	ARID3A	chr6:20213207-20214140	K562	blood:	n/a	n/a
21	POLR2A	chr6:20212169-20213411	GM12892	blood:	n/a	n/a
22	JUND	chr6:20212202-20214142	K562	blood:	n/a	n/a
23	HA-E2F1	chr6:20212278-20213475	MCF-7	breast:	n/a	chr6:20212662-20212669 chr6:20212732-20212747 chr6:20212928-20212935 chr6:20212889-20212899
24	POLR2A	chr6:20212110-20213386	GM18526	blood:	n/a	n/a
25	ATF2	chr6:20212757-20213399	GM12878	blood:	n/a	n/a
26	UBTF	chr6:20212149-20213980	K562	blood:	n/a	n/a
27	SMARCC1	chr6:20212205-20213690	Hela-S3	cervix:	n/a	n/a
28	CHD2	chr6:20212612-20213566	K562	blood:	n/a	chr6:20212928-20212935 chr6:20213019-20213029
29	POLR2A	chr6:20212408-20213960	K562	blood:	n/a	n/a
30	NR2F2	chr6:20212487-20213401	MCF-7	breast:	n/a	n/a
31	POLR2A	chr6:20212460-20213709	MCF10A-Er-Src	breast:	n/a	n/a
32	TRIM28	chr6:20212627-20213434	K562	blood:	n/a	chr6:20213099-20213107
33	POLR2A	chr6:20212315-20213417	K562	blood:	n/a	n/a
34	CTCF	chr6:20213200-20213350	HCPEpiC	choroid plexus:	n/a	n/a
35	NR2F2	chr6:20212029-20214154	K562	blood:	n/a	n/a
36	RCOR1	chr6:20211320-20214158	K562	blood:	n/a	n/a
37	STAT5A	chr6:20212202-20213469	GM12878	blood:	n/a	chr6:20212788-20212796 chr6:20213017-20213029 chr6:20213021-20213033
38	POLR2A	chr6:20212287-20213368	ECC-1	luminal epithelium:	n/a	n/a
39	HEY1	chr6:20212306-20213353	K562	blood:	n/a	chr6:20212825-20212840
40	POLR2A	chr6:20212795-20213363	GM12891	blood:	n/a	n/a
41	POLR2A	chr6:20212055-20213506	GM12878	blood:	n/a	n/a
42	TAF1	chr6:20212749-20213387	PFSK-1	brain:	n/a	n/a
43	RFX5	chr6:20211433-20213482	Hela-S3	cervix:	n/a	n/a
44	ELF1	chr6:20212118-20213443	MCF-7	breast:	n/a	chr6:20212894-20212903
45	POLR2A	chr6:20212729-20213365	GM12891	blood:	n/a	n/a
46	POLR2A	chr6:20212146-20213956	K562	blood:	n/a	n/a
47	CHD1	chr6:20212033-20213391	GM12878	blood:	n/a	chr6:20212928-20212935 chr6:20213019-20213029
48	RELA	chr6:20212090-20213686	GM15510	blood:	n/a	n/a
49	ZNF384	chr6:20212768-20214184	K562	blood:	n/a	n/a
50	TAL1	chr6:20212914-20213468	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:14664515..14665311-chr6:20212717..20213354,2	Hela-S3	cervix:
2	chr6:20208250..20214334-chr6:20400294..20406447,14	K562	blood:
3	chr6:20212989..20214883-chr6:20456758..20459141,2	K562	blood:
4	chr6:20208632..20214725-chr6:20400593..20405219,15	K562	blood:
5	chr6:20208057..20215931-chr6:20401288..20405953,13	MCF-7	breast:

Variant related genes	Relation type
MBOAT1	TF binding region
ENSG00000154124	Chromatin interaction
ENSG00000261360	Chromatin interaction
ENSG00000112242	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1077920	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536580	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1536581	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6928120	0.92[ASN][1000 genomes]
rs9350222	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9350223	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs9358312	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes];0.95[ASN][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	nsv1029729	chr6:20113226-20235122	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538155	chr6:20113226-20235122	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1027355	chr6:20207893-20261048	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr6:20210600-20213600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:20210600-20213800	Active TSS	Ovary	ovary
3	chr6:20211000-20213400	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr6:20211000-20213400	Active TSS	GM12878-XiMat	blood
5	chr6:20211000-20213600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr6:20211000-20213600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:20211000-20213600	Active TSS	Right Atrium	heart
8	chr6:20211200-20213400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:20211200-20213400	Active TSS	Brain Substantia Nigra	brain
10	chr6:20211200-20213400	Active TSS	Esophagus	oesophagus
11	chr6:20211200-20213400	Active TSS	Gastric	stomach
12	chr6:20211200-20213400	Active TSS	Small Intestine	intestine
13	chr6:20211200-20213600	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr6:20211400-20213400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:20211400-20213400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:20211400-20213400	Active TSS	Aorta	Aorta
17	chr6:20211400-20213400	Active TSS	Brain Hippocampus Middle	brain
18	chr6:20211400-20213400	Active TSS	Pancreas	Pancrea
19	chr6:20211400-20213600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:20211400-20213600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr6:20211600-20213400	Active TSS	Colon Smooth Muscle	Colon
22	chr6:20211600-20213400	Active TSS	Lung	lung
23	chr6:20211600-20213400	Active TSS	Placenta Amnion	Placenta Amnion
24	chr6:20211600-20213400	Active TSS	Stomach Smooth Muscle	stomach
25	chr6:20211600-20213400	Active TSS	A549	lung
26	chr6:20211600-20213600	Active TSS	Left Ventricle	heart
27	chr6:20211600-20213600	Active TSS	Right Ventricle	heart
28	chr6:20211800-20213400	Active TSS	Fetal Stomach	stomach
29	chr6:20211800-20213800	Active TSS	Psoas Muscle	Psoas
30	chr6:20212000-20213400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:20212000-20213600	Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:20212200-20213400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:20212400-20213400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:20212400-20213400	Active TSS	Spleen	Spleen
35	chr6:20212400-20213800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:20212600-20213400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:20212600-20213400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:20213000-20213400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:20213000-20213400	Bivalent/Poised TSS	Fetal Brain Male	brain
40	chr6:20213000-20213600	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr6:20213000-20213600	Flanking Active TSS	Placenta	Placenta
42	chr6:20213000-20213800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr6:20213000-20214000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr6:20213200-20213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:20213200-20213400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:20213200-20213400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
47	chr6:20213200-20213400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:20213200-20213400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:20213200-20213400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr6:20213200-20213400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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