Variant report

Variant	rs2277941
Chromosome Location	chr19:39108723-39108724
allele	A/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	POLR2A	chr19:39108430-39110088	ECC-1	luminal epithelium:	n/a	n/a
2	ELF1	chr19:39108360-39109112	GM12878	blood:	n/a	n/a
3	MAX	chr19:39108180-39110049	NB4	blood:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39108656-39108666 chr19:39109718-39109737 chr19:39108653-39108663 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
4	TCF12	chr19:39108502-39108846	GM12878	blood:	n/a	chr19:39108567-39108577
5	RUNX3	chr19:39107907-39110161	GM12878	blood:	n/a	n/a
6	RELA	chr19:39108050-39110036	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:39108374-39109607	GM12892	blood:	n/a	n/a
8	EP300	chr19:39108456-39109084	GM12878	blood:	n/a	n/a
9	RELA	chr19:39108503-39110090	GM18505	blood:	n/a	n/a
10	SP1	chr19:39108444-39109157	GM12878	blood:	n/a	chr19:39108867-39108876 chr19:39108867-39108877 chr19:39108866-39108878 chr19:39108868-39108877 chr19:39108710-39108722 chr19:39108868-39108881 chr19:39108710-39108722 chr19:39108866-39108878
11	BCLAF1	chr19:39108124-39109266	GM12878	blood:	n/a	chr19:39108867-39108876
12	POLR2A	chr19:39107935-39110102	GM12878	blood:	n/a	n/a
13	TCF12	chr19:39108662-39110703	A549	lung:	n/a	chr19:39110689-39110696
14	ZEB1	chr19:39108483-39109607	GM12878	blood:	n/a	n/a
15	EP300	chr19:39108177-39109112	GM12878	blood:	n/a	n/a
16	SIX5	chr19:39108632-39110279	A549	lung:	n/a	n/a
17	POLR2A	chr19:39108098-39110085	GM15510	blood:	n/a	n/a
18	POU2F2	chr19:39108499-39108814	GM12878	blood:	n/a	n/a
19	MTA3	chr19:39107759-39110618	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:39108616-39111427	K562	blood:	n/a	n/a
21	EBF1	chr19:39108435-39109025	GM12878	blood:	n/a	chr19:39108768-39108777 chr19:39108723-39108734 chr19:39108768-39108778
22	FOXM1	chr19:39108303-39109013	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:39108499-39110186	HL-60	blood:	n/a	n/a
24	MAX	chr19:39108005-39110007	GM12878	blood:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39108656-39108666 chr19:39109718-39109737 chr19:39108653-39108663 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
25	POLR2A	chr19:39107886-39110202	GM12892	blood:	n/a	n/a
26	SIN3A	chr19:39108125-39110525	GM12878	blood:	n/a	chr19:39109722-39109731 chr19:39109309-39109318 chr19:39110041-39110055
27	POLR2A	chr19:39107795-39111328	GM12878	blood:	n/a	n/a
28	SIN3AK20	chr19:39108443-39111312	PANC-1	pancreas:	n/a	n/a
29	MYC	chr19:39108265-39110035	NB4	blood:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39108656-39108666 chr19:39109718-39109737 chr19:39108653-39108663 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
30	RELA	chr19:39108456-39109162	GM18526	blood:	n/a	n/a
31	POLR2A	chr19:39108040-39109165	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:39107997-39110181	GM12878	blood:	n/a	n/a
33	RELA	chr19:39108007-39110024	GM19193	blood:	n/a	n/a
34	POLR2A	chr19:39108007-39110122	Raji	blood:	n/a	n/a
35	YY1	chr19:39107869-39108880	GM12878	blood:	n/a	chr19:39107953-39107964 chr19:39108868-39108877
36	ZBTB7A	chr19:39108442-39108788	K562	blood:	n/a	n/a
37	RCOR1	chr19:39108060-39110038	GM12878	blood:	n/a	n/a
38	EBF1	chr19:39108418-39109085	GM12878	blood:	n/a	chr19:39108768-39108777 chr19:39108723-39108734 chr19:39108768-39108778
39	POLR2A	chr19:39108158-39113791	PANC-1	pancreas:	n/a	n/a
40	CHD2	chr19:39108429-39109972	GM12878	blood:	n/a	n/a
41	RELA	chr19:39108010-39110032	GM15510	blood:	n/a	n/a
42	CUX1	chr19:39108529-39109395	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:39107991-39110092	GM19099	blood:	n/a	n/a
44	POLR2A	chr19:39108155-39109187	GM12891	blood:	n/a	n/a
45	POLR2A	chr19:39108382-39110065	NB4	blood:	n/a	n/a
46	RELA	chr19:39108409-39110037	GM18951	blood:	n/a	n/a
47	POLR2A	chr19:39108539-39110828	K562	blood:	n/a	n/a
48	TCF3	chr19:39108513-39108776	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:39108025-39110142	GM18505	blood:	n/a	n/a
50	BHLHE40	chr19:39108509-39109104	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39108723-39108773	HRCEpiC	kidney:	n/a
2	chr19:39108723-39108773	HUVEC	blood vessel:	n/a
3	chr19:39108723-39108773	NHDF-neo	bronchial:	n/a
4	chr19:39108723-39108773	HCF	heart:	n/a
5	chr19:39108723-39108773	HRPEpiC	eye:	n/a
6	chr19:39108723-39108773	SK-N-MC	brain:	n/a
7	chr19:39108723-39108773	GM12892	blood:	n/a
8	chr19:39108723-39108773	K562	blood:	n/a
9	chr19:39108723-39108773	HepG2	liver:	n/a
10	chr19:39108723-39108773	Hepatocyte	liver:	n/a
11	chr19:39108723-39108773	GM06990	blood:	n/a
12	chr19:39108723-39108773	GM12878	blood:	n/a
13	chr19:39108723-39108773	GM19239	blood:	n/a
14	chr19:39108723-39108773	H1-hESC	embryonic stem cell:	embryo
15	chr19:39108723-39108773	HEK293	kidney:	embryo
16	chr19:39108723-39108773	CMK	blood:	n/a
17	chr19:39108723-39108773	NH-A	brain:	n/a
18	chr19:39108723-39108773	RPTEC	kidney:	n/a
19	chr19:39108723-39108773	HL-60	blood:	n/a
20	chr19:39108723-39108773	AG04449	skin:	fetal
21	chr19:39108723-39108773	BJ	skin:	n/a
22	chr19:39108723-39108773	AG09319	gingival:	n/a
23	chr19:39108723-39108773	AoSMC	blood vessel:	n/a
24	chr19:39108723-39108773	NHBE	bronchial:	n/a
25	chr19:39108723-39108773	HEEpiC	esophagus:	n/a
26	chr19:39108723-39108773	PANC-1	pancreas:	n/a
27	chr19:39108723-39108773	ovcar-3	ovarian:	n/a
28	chr19:39108723-39108773	HNPCEpiC	eye:	n/a
29	chr19:39108723-39108773	IMR90	lung:	fetal
30	chr19:39108723-39108773	Caco-2	colon:	n/a
31	chr19:39108723-39108773	Hela-S3	cervix:	n/a
32	chr19:39108723-39108773	AG10803	skin:	n/a
33	chr19:39108723-39108773	SKMC	muscle:	n/a
34	chr19:39108723-39108773	HAEpiC	amniotic membrane:	n/a
35	chr19:39108723-39108773	AG04450	lung:	fetal
36	chr19:39108723-39108773	MCF-7	breast:	n/a
37	chr19:39108723-39108773	T-47D	breast:	n/a
38	chr19:39108723-39108773	Jurkat	blood:	n/a
39	chr19:39108723-39108773	SAEC	small airway:	n/a
40	chr19:39108723-39108773	HCM	heart:	n/a
41	chr19:39108723-39108773	SK-N-SH_RA	brain:	n/a
42	chr19:39108723-39108773	HCPEpiC	choroid plexus:	n/a
43	chr19:39108723-39108773	SK-N-SH	brain:	n/a
44	chr19:39108723-39108773	HCT-116	colon:	n/a
45	chr19:39108723-39108773	PrEC	prostate:	n/a
46	chr19:39108723-39108773	GM12891	blood:	n/a
47	chr19:39108723-39108773	HMEC	breast:	n/a
48	chr19:39108723-39108773	ProgFib	skin:	n/a
49	chr19:39108723-39108773	HPAEpiC	pulmonary alveolar:	n/a
50	chr19:39108723-39108773	NB4	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38878822..38880604-chr19:39108487..39110318,2	MCF-7	breast:
2	chr19:39106830..39111691-chr19:39117375..39123240,7	MCF-7	breast:
3	chr19:39086098..39088583-chr19:39106611..39110096,5	K562	blood:
4	chr19:39108184..39110512-chr19:39341783..39344242,3	MCF-7	breast:
5	chr19:39103433..39106687-chr19:39106977..39109796,8	K562	blood:
6	chr19:39107241..39111219-chr19:39136508..39140596,7	K562	blood:
7	chr19:39102966..39104689-chr19:39107783..39109776,2	MCF-7	breast:
8	chr19:39108057..39110372-chr19:39339414..39342268,3	K562	blood:
9	chr19:39024830..39027065-chr19:39108421..39111246,2	MCF-7	breast:
10	chr19:39103495..39106423-chr19:39106849..39111061,4	MCF-7	breast:
11	chr19:39101758..39105983-chr19:39106668..39109959,5	K562	blood:
12	chr19:39108167..39112213-chr19:39136508..39140596,7	K562	blood:
13	chr19:39108186..39111004-chr19:39340137..39342268,2	K562	blood:

Variant related genes	Relation type
EIF3K	TF binding region
MAP4K1	TF binding region
EIF3K	CpG island
MAP4K1	CpG island
ENSG00000178982	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000267291	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12977252	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2232992	0.90[ASN][1000 genomes]
rs2232997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34780679	0.90[ASN][1000 genomes]
rs34979870	0.82[ASN][1000 genomes]
rs57230275	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2277941	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39087400-39108800	Weak transcription	Right Atrium	heart
2	chr19:39092600-39109000	Weak transcription	Small Intestine	intestine
3	chr19:39106200-39108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr19:39106800-39109600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr19:39107000-39109200	Flanking Active TSS	Dnd41	blood
6	chr19:39107000-39109400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr19:39107000-39109600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr19:39107200-39109400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:39107200-39109600	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr19:39107400-39108800	Active TSS	Duodenum Mucosa	Duodenum
11	chr19:39107400-39109000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:39107600-39110200	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr19:39107800-39108800	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr19:39107800-39109400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr19:39107800-39109400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr19:39107800-39110600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:39107800-39111000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:39108000-39108800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:39108000-39108800	Active TSS	Brain Substantia Nigra	brain
20	chr19:39108000-39108800	Enhancers	Fetal Muscle Trunk	muscle
21	chr19:39108000-39108800	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr19:39108000-39109000	Enhancers	Lung	lung
23	chr19:39108000-39109000	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr19:39108000-39109400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr19:39108000-39109400	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr19:39108000-39109400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:39108000-39109400	Flanking Active TSS	Fetal Thymus	thymus
28	chr19:39108000-39109600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr19:39108000-39109600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:39108000-39110200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:39108200-39108800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr19:39108200-39108800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:39108200-39108800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr19:39108200-39108800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:39108200-39108800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:39108200-39108800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:39108200-39108800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:39108200-39108800	Enhancers	Liver	Liver
39	chr19:39108200-39108800	Enhancers	Brain Germinal Matrix	brain
40	chr19:39108200-39108800	Active TSS	Brain Hippocampus Middle	brain
41	chr19:39108200-39108800	Enhancers	Fetal Stomach	stomach
42	chr19:39108200-39108800	Enhancers	Stomach Mucosa	stomach
43	chr19:39108200-39109000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr19:39108200-39109400	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr19:39108200-39109600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr19:39108400-39108800	Active TSS	Primary B cells from peripheral blood	blood
47	chr19:39108400-39108800	Active TSS	Primary T cells from cord blood	blood
48	chr19:39108400-39108800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:39108400-39108800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39108400-39108800	Enhancers	Fetal Brain Male	brain

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