Variant report

Variant	rs3799963
Chromosome Location	chr6:44231479-44231480
allele	C/G/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	NFATC1	chr6:44230615-44232531	GM12878	blood:	n/a	n/a
2	BCLAF1	chr6:44229967-44232867	GM12878	blood:	n/a	chr6:44232448-44232457 chr6:44231117-44231126 chr6:44230517-44230526 chr6:44231116-44231125
3	TAF1	chr6:44230828-44231826	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:44231075-44231578	HL-60	blood:	n/a	n/a
5	ZNF143	chr6:44230193-44231629	GM12878	blood:	n/a	chr6:44230227-44230246 chr6:44231088-44231106
6	EP300	chr6:44230918-44231515	GM12878	blood:	n/a	n/a
7	YY1	chr6:44230835-44232368	GM12878	blood:	n/a	n/a
8	RELA	chr6:44230400-44233646	GM18505	blood:	n/a	chr6:44230761-44230770 chr6:44230761-44230770 chr6:44231328-44231337 chr6:44231328-44231337
9	IRF4	chr6:44231062-44231572	GM12878	blood:	n/a	n/a
10	USF2	chr6:44230509-44231645	GM12878	blood:	n/a	n/a
11	YY1	chr6:44231151-44231720	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:44213452-44233528	GM12892	blood:	n/a	n/a
13	EGR1	chr6:44231279-44231509	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:44231419-44231545	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:44230986-44231620	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr6:44231146-44233514	Raji	blood:	n/a	n/a
17	POLR2A	chr6:44213372-44233644	GM12891	blood:	n/a	n/a
18	STAT5A	chr6:44229584-44233087	GM12878	blood:	n/a	chr6:44231139-44231150 chr6:44230531-44230543 chr6:44231312-44231320 chr6:44231460-44231468 chr6:44229749-44229761
19	TAL1	chr6:44231421-44231641	K562	blood:	n/a	n/a
20	EGR1	chr6:44231047-44231546	GM12878	blood:	n/a	chr6:44231233-44231246
21	ELF1	chr6:44231297-44231575	HepG2	liver:	n/a	chr6:44231408-44231421
22	SPI1	chr6:44230973-44231661	HL-60	blood:	n/a	chr6:44231310-44231323 chr6:44231095-44231108
23	JUND	chr6:44231444-44231488	K562	blood:	n/a	n/a
24	POLR2A	chr6:44213416-44233519	GM12878	blood:	n/a	n/a
25	TEAD4	chr6:44231179-44231489	H1-hESC	embryonic stem cell:	n/a	n/a
26	CUX1	chr6:44230844-44231531	GM12878	blood:	n/a	n/a
27	SPI1	chr6:44231210-44231559	K562	blood:	n/a	chr6:44231310-44231323
28	CEBPB	chr6:44230373-44232307	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:44229240-44233577	GM18951	blood:	n/a	n/a
30	POLR2A	chr6:44229697-44233440	GM12891	blood:	n/a	n/a
31	POLR2A	chr6:44213785-44233471	GM12878	blood:	n/a	n/a
32	MAX	chr6:44230802-44231598	GM12878	blood:	n/a	n/a
33	MYC	chr6:44231239-44231505	HUVEC	blood vessel:	n/a	n/a
34	WRNIP1	chr6:44229636-44233069	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:44213479-44233557	GM12892	blood:	n/a	n/a
36	NFATC1	chr6:44230324-44231752	GM12878	blood:	n/a	n/a
37	STAT3	chr6:44231217-44231505	GM12878	blood:	n/a	chr6:44231312-44231320 chr6:44231460-44231468
38	STAT5A	chr6:44231305-44232462	GM12878	blood:	n/a	chr6:44231312-44231320 chr6:44231460-44231468
39	POLR2A	chr6:44229166-44233419	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:44231095-44231932	HepG2	liver:	n/a	n/a
41	BCL11A	chr6:44230897-44231564	GM12878	blood:	n/a	chr6:44231117-44231126 chr6:44231116-44231125
42	SPI1	chr6:44231180-44231583	HL-60	blood:	n/a	chr6:44231310-44231323
43	POLR2A	chr6:44231289-44232247	K562	blood:	n/a	n/a
44	BHLHE40	chr6:44230672-44231600	GM12878	blood:	n/a	n/a
45	ELK1	chr6:44231033-44231531	GM12878	blood:	n/a	n/a
46	ELF1	chr6:44230296-44231760	GM12878	blood:	n/a	chr6:44230408-44230420 chr6:44231408-44231421
47	CHD2	chr6:44230574-44231666	GM12878	blood:	n/a	n/a
48	MTA3	chr6:44229970-44232487	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:44229138-44233380	GM12891	blood:	n/a	n/a
50	POLR2A	chr6:44229960-44233576	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:44230152..44232181-chr6:44314660..44317132,2	K562	blood:
2	chr6:44093102..44095527-chr6:44231141..44233414,2	MCF-7	breast:
3	chr6:44229152..44231602-chr6:44233591..44236343,2	MCF-7	breast:
4	chr6:44231291..44234957-chr6:44353668..44356659,3	K562	blood:
5	chr6:44229471..44232092-chr6:44306709..44308642,2	K562	blood:
6	chr6:44231038..44232613-chr6:44324108..44326590,2	K562	blood:
7	chr6:44100637..44102842-chr6:44230503..44233422,2	MCF-7	breast:
8	chr6:43624198..43626185-chr6:44230029..44232355,2	K562	blood:
9	chr6:44231156..44234544-chr6:44279395..44281173,3	MCF-7	breast:

Variant related genes	Relation type
NFKBIE	TF binding region
ENSG00000096401	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000137216	Chromatin interaction
ENSG00000180992	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1044690	0.84[ASN][1000 genomes]
rs2233424	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233433	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2233434	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236500	0.91[EUR][1000 genomes]
rs28362854	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362855	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362856	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362859	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35623954	0.85[EUR][1000 genomes]
rs3734708	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3734709	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41282670	0.85[EUR][1000 genomes]
rs60453984	0.82[EUR][1000 genomes]
rs61742784	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6458377	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885855	chr6:44223010-44231479	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
12	nsv885856	chr6:44223010-44232920	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
13	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44225600-44232600	Weak transcription	Aorta	Aorta
2	chr6:44229400-44232800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:44230000-44231600	Enhancers	Fetal Lung	lung
4	chr6:44230000-44232000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:44230000-44232000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:44230000-44233200	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr6:44230200-44232800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr6:44230200-44233400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:44230400-44231600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:44230400-44231600	Enhancers	Fetal Heart	heart
11	chr6:44230400-44231800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:44230400-44231800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
13	chr6:44230400-44231800	Enhancers	Fetal Brain Male	brain
14	chr6:44230400-44232200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:44230400-44232800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr6:44230400-44232800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr6:44230400-44232800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:44230400-44232800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:44230400-44232800	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr6:44230400-44232800	Flanking Active TSS	HUVEC	blood vessel
21	chr6:44230400-44233000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr6:44230400-44233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:44230400-44233000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr6:44230400-44233000	Flanking Active TSS	Placenta	Placenta
25	chr6:44230400-44233200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:44230600-44231600	Flanking Active TSS	HepG2	liver
27	chr6:44230600-44231600	Enhancers	NHDF-Ad	bronchial
28	chr6:44230600-44231800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr6:44230600-44232200	Enhancers	Left Ventricle	heart
30	chr6:44230600-44232400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr6:44230600-44232400	Enhancers	Ovary	ovary
32	chr6:44230600-44232600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr6:44230600-44232600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:44230600-44232600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr6:44230600-44232600	Flanking Active TSS	Esophagus	oesophagus
36	chr6:44230600-44232600	Flanking Active TSS	NHEK	skin
37	chr6:44230600-44232800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr6:44230600-44232800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr6:44230600-44232800	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr6:44230600-44232800	Flanking Active TSS	HMEC	breast
41	chr6:44230600-44233000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr6:44230600-44233000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:44230600-44233000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:44230600-44233000	Flanking Active TSS	Liver	Liver
45	chr6:44230600-44233000	Flanking Active TSS	Colonic Mucosa	Colon
46	chr6:44230600-44233000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr6:44230600-44233000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr6:44230800-44231600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr6:44230800-44231800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr6:44230800-44231800	Enhancers	Psoas Muscle	Psoas

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