Variant report

Variant	rs3806980
Chromosome Location	chr6:74231223-74231224
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	CEBPD	chr6:74230374-74231361	K562	blood:	n/a	n/a
2	CREB1	chr6:74229772-74231695	K562	blood:	n/a	chr6:74231556-74231569
3	POLR2A	chr6:74227757-74231735	U87	brain:	n/a	n/a
4	YY1	chr6:74229744-74231727	ECC-1	luminal epithelium:	n/a	chr6:74230146-74230154 chr6:74230148-74230156 chr6:74230109-74230119 chr6:74230282-74230296 chr6:74230145-74230155 chr6:74230145-74230167 chr6:74230511-74230525
5	FOXP2	chr6:74231135-74231543	SK-N-MC	brain:	n/a	n/a
6	YY1	chr6:74229802-74231651	H1-hESC	embryonic stem cell:	n/a	chr6:74230146-74230154 chr6:74230148-74230156 chr6:74230109-74230119 chr6:74230282-74230296 chr6:74230145-74230155 chr6:74230145-74230167 chr6:74230511-74230525
7	ZNF143	chr6:74230465-74232162	K562	blood:	n/a	chr6:74231121-74231139
8	REST	chr6:74229777-74231643	HL-60	blood:	n/a	chr6:74230129-74230142 chr6:74230240-74230253
9	RCOR1	chr6:74229861-74231975	K562	blood:	n/a	n/a
10	RCOR1	chr6:74229889-74231677	K562	blood:	n/a	n/a
11	POLR2A	chr6:74227580-74231982	MCF10A-Er-Src	breast:	n/a	n/a
12	ELF1	chr6:74229896-74231622	GM12878	blood:	n/a	chr6:74230510-74230522
13	BHLHE40	chr6:74229992-74231613	HepG2	liver:	n/a	chr6:74230508-74230524 chr6:74231107-74231123
14	RELA	chr6:74229260-74232316	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:74228816-74232047	HepG2	liver:	n/a	n/a
16	PML	chr6:74229072-74231655	K562	blood:	n/a	n/a
17	TAF1	chr6:74230416-74231599	HepG2	liver:	n/a	n/a
18	TEAD4	chr6:74229682-74231466	ECC-1	luminal epithelium:	n/a	n/a
19	GATA3	chr6:74229580-74231701	A549	lung:	n/a	n/a
20	BHLHE40	chr6:74229893-74232231	GM12878	blood:	n/a	chr6:74230508-74230524 chr6:74231107-74231123
21	YY1	chr6:74229784-74231677	K562	blood:	n/a	chr6:74230146-74230154 chr6:74230148-74230156 chr6:74230109-74230119 chr6:74230282-74230296 chr6:74230145-74230155 chr6:74230145-74230167 chr6:74230511-74230525
22	TEAD4	chr6:74230443-74231309	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAZ	chr6:74229755-74231968	GM12878	blood:	n/a	chr6:74230793-74230803 chr6:74231000-74231010 chr6:74230504-74230513
24	POLR2A	chr6:74227654-74232081	GM12892	blood:	n/a	n/a
25	TBP	chr6:74230390-74232271	Hela-S3	cervix:	n/a	n/a
26	E2F4	chr6:74229850-74231595	K562	blood:	n/a	chr6:74230292-74230302 chr6:74231002-74231014
27	CHD1	chr6:74228853-74232500	IMR90	lung:	n/a	chr6:74230887-74230897 chr6:74229942-74229952
28	ELF1	chr6:74230531-74231534	HepG2	liver:	n/a	n/a
29	NR2F2	chr6:74229697-74231884	K562	blood:	n/a	n/a
30	ZNF143	chr6:74229906-74231648	H1-hESC	embryonic stem cell:	n/a	chr6:74231121-74231139
31	POLR2A	chr6:74229040-74231763	ProgFib	skin:	n/a	n/a
32	SMC3	chr6:74229753-74231988	Hela-S3	cervix:	n/a	chr6:74230493-74230500
33	POLR2A	chr6:74229895-74231564	MCF-7	breast:	n/a	n/a
34	POLR2A	chr6:74227647-74232257	K562	blood:	n/a	n/a
35	ZKSCAN1	chr6:74230473-74231716	Hela-S3	cervix:	n/a	n/a
36	NFIC	chr6:74229922-74231672	HepG2	liver:	n/a	n/a
37	CREB1	chr6:74229688-74231838	HepG2	liver:	n/a	chr6:74231556-74231569
38	MAX	chr6:74229743-74231746	SK-N-SH	brain:	n/a	chr6:74230793-74230803 chr6:74231000-74231010 chr6:74230504-74230513
39	TAF1	chr6:74230284-74231586	PFSK-1	brain:	n/a	n/a
40	SIN3A	chr6:74229757-74231716	GM12878	blood:	n/a	chr6:74230994-74231005 chr6:74229998-74230011
41	NFIC	chr6:74229759-74231788	GM12878	blood:	n/a	n/a
42	CREB1	chr6:74230500-74231759	H1-hESC	embryonic stem cell:	n/a	chr6:74231556-74231569
43	HNF4G	chr6:74230500-74231337	HepG2	liver:	n/a	n/a
44	BHLHE40	chr6:74229900-74231612	K562	blood:	n/a	chr6:74230508-74230524 chr6:74231107-74231123
45	ZNF143	chr6:74229889-74231464	Hela-S3	cervix:	n/a	chr6:74231121-74231139
46	PBX3	chr6:74230360-74231729	SK-N-SH	brain:	n/a	chr6:74230935-74230955
47	EP300	chr6:74230594-74231832	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:74227716-74232005	HepG2	liver:	n/a	n/a
49	HCFC1	chr6:74229302-74232137	Hela-S3	cervix:	n/a	n/a
50	RELA	chr6:74229314-74231856	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:74230158..74233335-chr6:74327185..74331083,5	K562	blood:
2	chr6:74228897..74233348-chr6:76310739..76313863,5	K562	blood:
3	chr6:74221323..74236726-chr6:74306065..74338770,101	K562	blood:
4	chr6:74228067..74234767-chr6:74357105..74365312,16	MCF-7	breast:
5	chr6:74229352..74231539-chr6:75915151..75917818,2	MCF-7	breast:
6	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
7	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
8	chr1:205599949..205601241-chr6:74230209..74231496,3	Hela-S3	cervix:
9	chr5:175814751..175816394-chr6:74229187..74232142,2	MCF-7	breast:
10	chr6:74018617..74020402-chr6:74229038..74231578,2	K562	blood:
11	chr22:45559355..45561489-chr6:74229650..74231548,2	MCF-7	breast:
12	chr21:34915060..34915854-chr6:74230700..74231468,2	HCT-116	colon:
13	chr19:1652085..1652812-chr6:74230264..74231263,2	Hela-S3	cervix:
14	chr12:51632180..51632977-chr6:74230623..74231461,2	Hela-S3	cervix:
15	chr6:74228702..74232744-chr6:74360665..74366385,13	MCF-7	breast:
16	chr15:75747614..75748882-chr6:74230241..74231226,3	Hela-S3	cervix:
17	chr6:74229402..74231607-chr6:76310929..76313785,2	K562	blood:
18	chr11:47585806..47587545-chr6:74230961..74233222,2	K562	blood:
19	chr6:74169192..74174230-chr6:74229143..74231785,9	K562	blood:
20	chr19:12900751..12902436-chr6:74228731..74231614,2	MCF-7	breast:
21	chr16:75271441..75274374-chr6:74228830..74231678,2	MCF-7	breast:
22	chr6:74161775..74163563-chr6:74231007..74233412,2	MCF-7	breast:
23	chr16:3070201..3071071-chr6:74230886..74231774,2	Hela-S3	cervix:
24	chr6:27112481..27114921-chr6:74229958..74232604,2	K562	blood:
25	chr20:26188395..26190565-chr6:74228700..74231505,2	MCF-7	breast:
26	chr6:74230395..74231262-chr7:44613185..44614138,2	Hela-S3	cervix:
27	chr6:74229302..74231632-chr8:103666566..103668459,2	MCF-7	breast:
28	chr6:73972686..73974360-chr6:74230027..74232988,2	MCF-7	breast:
29	chr2:110370972..110371523-chr6:74230603..74231263,2	Hela-S3	cervix:
30	chr6:74229165..74233433-chr6:74353361..74356645,5	MCF-7	breast:
31	chr1:16161734..16162465-chr6:74230724..74231287,2	Hela-S3	cervix:
32	chr6:74170147..74173171-chr6:74228405..74233047,5	K562	blood:
33	chr6:74157393..74162572-chr6:74229200..74231801,6	MCF-7	breast:
34	chr6:74201956..74203659-chr6:74230249..74231755,2	K562	blood:
35	chr6:37400721..37403243-chr6:74228826..74231547,2	K562	blood:
36	chr6:74169360..74174580-chr6:74228668..74231530,6	MCF-7	breast:
37	chr6:74189673..74193242-chr6:74229143..74231708,4	MCF-7	breast:

Variant related genes	Relation type
EEF1A1	TF binding region
ENSG00000229862	TF binding region
ENSG00000227195	Chromatin interaction
ENSG00000110536	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000243501	Chromatin interaction
ENSG00000218459	Chromatin interaction
ENSG00000093000	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000050820	Chromatin interaction
ENSG00000226328	Chromatin interaction
ENSG00000119899	Chromatin interaction
ENSG00000112701	Chromatin interaction
ENSG00000006327	Chromatin interaction
ENSG00000159140	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000186522	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000135314	Chromatin interaction
ENSG00000223821	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000158711	Chromatin interaction
ENSG00000136271	Chromatin interaction
ENSG00000146066	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000229852	Chromatin interaction
ENSG00000159131	Chromatin interaction
ENSG00000048162	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000071564	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000111799	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000137200	Chromatin interaction
ENSG00000179743	Chromatin interaction
ENSG00000263378	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11965436	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11968395	0.85[EUR][1000 genomes]
rs11969010	0.85[EUR][1000 genomes]
rs12198839	0.88[ASN][1000 genomes]
rs56375536	0.91[AMR][1000 genomes]
rs72951364	1.00[EUR][1000 genomes]
rs72953359	0.92[EUR][1000 genomes]
rs72960023	0.85[EUR][1000 genomes]
rs72960035	0.85[EUR][1000 genomes]
rs72960044	1.00[EUR][1000 genomes]
rs72960049	1.00[EUR][1000 genomes]
rs72961942	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
9	nsv5350	chr6:74221995-74267088	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
10	nsv886159	chr6:74223153-74275405	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
11	nsv463153	chr6:74229258-74290291	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
12	nsv603693	chr6:74229258-74290291	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3806980	DDX43	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74225000-74231600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:74227200-74232000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:74227800-74231800	Active TSS	Placenta Amnion	Placenta Amnion
4	chr6:74227800-74233800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:74228000-74231800	Active TSS	Right Ventricle	heart
6	chr6:74228400-74231600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
7	chr6:74228600-74232000	Active TSS	Fetal Brain Female	brain
8	chr6:74228800-74231800	Active TSS	Esophagus	oesophagus
9	chr6:74229000-74231600	Active TSS	Gastric	stomach
10	chr6:74229000-74232000	Active TSS	Aorta	Aorta
11	chr6:74229200-74231600	Active TSS	Left Ventricle	heart
12	chr6:74229200-74232000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:74229200-74232000	Active TSS	Small Intestine	intestine
14	chr6:74229400-74231600	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr6:74229400-74231600	Active TSS	Lung	lung
16	chr6:74229400-74231600	Active TSS	Pancreas	Pancrea
17	chr6:74229400-74231600	Active TSS	Thymus	Thymus
18	chr6:74229400-74231800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:74229400-74232000	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr6:74229400-74232200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr6:74229600-74231600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:74229600-74231800	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr6:74229600-74231800	Active TSS	Colonic Mucosa	Colon
24	chr6:74229600-74231800	Active TSS	Colon Smooth Muscle	Colon
25	chr6:74229600-74231800	Active TSS	Ovary	ovary
26	chr6:74229600-74231800	Active TSS	Stomach Mucosa	stomach
27	chr6:74229600-74232000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:74229800-74231400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:74229800-74231400	Bivalent/Poised TSS	Psoas Muscle	Psoas
30	chr6:74229800-74231400	Active TSS	Spleen	Spleen
31	chr6:74229800-74231600	Active TSS	Primary T cells from cord blood	blood
32	chr6:74229800-74231600	Active TSS	Primary hematopoietic stem cells	blood
33	chr6:74229800-74231600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr6:74229800-74231600	Active TSS	Brain Germinal Matrix	brain
35	chr6:74229800-74231600	Active TSS	Fetal Heart	heart
36	chr6:74229800-74231800	Active TSS	Primary monocytes fromperipheralblood	blood
37	chr6:74229800-74231800	Active TSS	Brain Anterior Caudate	brain
38	chr6:74229800-74231800	Active TSS	Brain Cingulate Gyrus	brain
39	chr6:74229800-74231800	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr6:74230000-74231400	Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr6:74230000-74231400	Active TSS	Primary B cells from peripheral blood	blood
42	chr6:74230000-74231400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:74230000-74231400	Transcr. at gene 5' and 3'	Right Atrium	heart
44	chr6:74230000-74231400	Bivalent/Poised TSS	HepG2	liver
45	chr6:74230000-74231600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:74230000-74231600	Active TSS	Primary B cells from cord blood	blood
47	chr6:74230000-74231600	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr6:74230000-74231600	Active TSS	Adipose Nuclei	Adipose
49	chr6:74230000-74231600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr6:74230000-74231600	Active TSS	Fetal Kidney	kidney

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