Variant report

Variant	rs2232997
Chromosome Location	chr19:39109975-39109976
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	USF1	chr19:39109291-39110078	A549	lung:	n/a	chr19:39109721-39109734
2	CREB1	chr19:39109524-39110068	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr19:39109652-39110018	K562	blood:	n/a	n/a
4	MAX	chr19:39109328-39110073	A549	lung:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39109718-39109737 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
5	IRF1	chr19:39109266-39110365	K562	blood:	n/a	chr19:39109809-39109829 chr19:39110327-39110341 chr19:39109599-39109613 chr19:39109809-39109822
6	POLR2A	chr19:39108430-39110088	ECC-1	luminal epithelium:	n/a	n/a
7	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
8	POLR2A	chr19:39109251-39110069	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:39109136-39110311	PFSK-1	brain:	n/a	n/a
10	IRF1	chr19:39109315-39110088	K562	blood:	n/a	chr19:39109809-39109829 chr19:39109599-39109613 chr19:39109809-39109822
11	NRF1	chr19:39109107-39109986	SK-N-SH	brain:	n/a	chr19:39109690-39109701 chr19:39109626-39109635 chr19:39109624-39109638 chr19:39109687-39109701 chr19:39109624-39109635 chr19:39109690-39109699 chr19:39109624-39109635 chr19:39109603-39109612
12	MXI1	chr19:39109279-39110103	HepG2	liver:	n/a	chr19:39109722-39109731
13	POLR2A	chr19:39109266-39110041	HepG2	liver:	n/a	n/a
14	USF1	chr19:39109285-39110163	A549	lung:	n/a	chr19:39109721-39109734
15	GTF2F1	chr19:39108993-39109984	H1-hESC	embryonic stem cell:	n/a	n/a
16	RUNX3	chr19:39107907-39110161	GM12878	blood:	n/a	n/a
17	SIN3AK20	chr19:39109198-39110098	H1-hESC	embryonic stem cell:	n/a	n/a
18	RELA	chr19:39108050-39110036	GM12891	blood:	n/a	n/a
19	RELA	chr19:39108503-39110090	GM18505	blood:	n/a	n/a
20	MYC	chr19:39109434-39110048	HUVEC	blood vessel:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39109718-39109737 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
21	MXI1	chr19:39109433-39109975	K562	blood:	n/a	chr19:39109722-39109731
22	TCF12	chr19:39109181-39110161	A549	lung:	n/a	n/a
23	POLR2A	chr19:39108990-39110165	HUVEC	blood vessel:	n/a	n/a
24	TCF7L2	chr19:39109471-39109984	PANC-1	pancreas:	n/a	n/a
25	YY1	chr19:39109307-39110020	SK-N-SH_RA	brain:	n/a	chr19:39109603-39109612
26	MYC	chr19:39109317-39109982	MCF10A-Er-Src	breast:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39109718-39109737 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
27	POLR2A	chr19:39107935-39110102	GM12878	blood:	n/a	n/a
28	TCF12	chr19:39108662-39110703	A549	lung:	n/a	chr19:39110689-39110696
29	POU2F2	chr19:39109651-39110086	GM12891	blood:	n/a	n/a
30	HCFC1	chr19:39109233-39110233	Hela-S3	cervix:	n/a	n/a
31	SIX5	chr19:39108632-39110279	A549	lung:	n/a	n/a
32	MYC	chr19:39109394-39110016	MCF-7	breast:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39109718-39109737 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
33	POLR2A	chr19:39109246-39110062	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIX5	chr19:39108964-39110077	A549	lung:	n/a	n/a
35	POLR2A	chr19:39108098-39110085	GM15510	blood:	n/a	n/a
36	MTA3	chr19:39109624-39110056	GM12878	blood:	n/a	n/a
37	MTA3	chr19:39107759-39110618	GM12878	blood:	n/a	n/a
38	MAX	chr19:39109333-39110025	K562	blood:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39109718-39109737 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
39	TAF1	chr19:39109650-39110053	GM12891	blood:	n/a	n/a
40	POLR2A	chr19:39108616-39111427	K562	blood:	n/a	n/a
41	EP300	chr19:39108886-39110695	A549	lung:	n/a	n/a
42	MYC	chr19:39109352-39110025	MCF-7	breast:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39109718-39109737 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
43	GABPA	chr19:39109568-39110041	Hela-S3	cervix:	n/a	chr19:39109690-39109701 chr19:39109626-39109635 chr19:39109624-39109638 chr19:39109687-39109701 chr19:39109690-39109699 chr19:39109624-39109635 chr19:39109603-39109612
44	ATF3	chr19:39109448-39110001	GM12878	blood:	n/a	chr19:39109603-39109612
45	PML	chr19:39109233-39110081	MCF-7	breast:	n/a	chr19:39110072-39110080
46	ZBTB33	chr19:39109398-39110087	A549	lung:	n/a	n/a
47	POLR2A	chr19:39109183-39110195	H1-neurons	neurons:	n/a	n/a
48	CREB1	chr19:39109341-39110162	HepG2	liver:	n/a	n/a
49	FOXP2	chr19:39109532-39110016	SK-N-MC	brain:	n/a	n/a
50	KAP1	chr19:39109228-39110074	U2OS	brain:	n/a	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	chr19:39109034..39110948-chr19:39138125..39139962,2	MCF-7	breast:
6	chr19:39107241..39111219-chr19:39136508..39140596,7	K562	blood:
7	chr19:39108057..39110372-chr19:39339414..39342268,3	K562	blood:
8	chr19:39024830..39027065-chr19:39108421..39111246,2	MCF-7	breast:
9	chr19:39103495..39106423-chr19:39106849..39111061,4	MCF-7	breast:
10	chr19:39109264..39111637-chr19:39122200..39124366,4	MCF-7	breast:
11	chr19:39108167..39112213-chr19:39136508..39140596,7	K562	blood:
12	chr19:39108186..39111004-chr19:39340137..39342268,2	K562	blood:

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

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12972987	0.89[MEX][hapmap];0.84[MKK][hapmap]
rs12977252	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17589359	0.84[MKK][hapmap]
rs17708009	1.00[YRI][hapmap]
rs2228068	1.00[YRI][hapmap]
rs2232992	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2277941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287728	0.89[MEX][hapmap];0.87[MKK][hapmap]
rs34780679	0.90[ASN][1000 genomes]
rs34979870	0.82[ASN][1000 genomes]
rs57230275	0.84[AFR][1000 genomes]
rs7251456	0.85[CEU][hapmap]
rs732135	1.00[ASW][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2232997	EIF3K	Cis_1M	lymphoblastoid	RTeQTL
rs2232997	KCNK6	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39107600-39110200	Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr19:39107800-39110600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:39107800-39111000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:39108000-39110200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:39108400-39110400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr19:39108400-39110400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:39108400-39110600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:39108400-39111000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr19:39108800-39110200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:39108800-39110400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr19:39108800-39110400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:39108800-39110400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:39108800-39110400	Active TSS	Fetal Kidney	kidney
14	chr19:39108800-39110400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:39108800-39110400	Active TSS	HSMM	muscle
16	chr19:39109000-39110200	Active TSS	Thymus	Thymus
17	chr19:39109000-39110400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:39109000-39110400	Active TSS	Left Ventricle	heart
19	chr19:39109000-39110400	Active TSS	Ovary	ovary
20	chr19:39109000-39110800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:39109200-39110200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:39109200-39110200	Active TSS	Primary T cells from cord blood	blood
23	chr19:39109200-39110200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:39109200-39110200	Active TSS	Brain Angular Gyrus	brain
25	chr19:39109200-39110200	Active TSS	Brain Anterior Caudate	brain
26	chr19:39109200-39110200	Active TSS	Brain Cingulate Gyrus	brain
27	chr19:39109200-39110200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr19:39109200-39110200	Active TSS	Colon Smooth Muscle	Colon
29	chr19:39109200-39110200	Active TSS	Fetal Brain Female	brain
30	chr19:39109200-39110200	Active TSS	Dnd41	blood
31	chr19:39109200-39110400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:39109200-39110400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:39109200-39110400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:39109200-39110400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:39109200-39110400	Active TSS	Aorta	Aorta
36	chr19:39109200-39110400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:39109200-39110400	Active TSS	Brain Substantia Nigra	brain
38	chr19:39109200-39110400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr19:39109200-39110400	Active TSS	Esophagus	oesophagus
40	chr19:39109200-39110400	Active TSS	Fetal Lung	lung
41	chr19:39109200-39110400	Active TSS	Gastric	stomach
42	chr19:39109200-39110400	Active TSS	Lung	lung
43	chr19:39109200-39110400	Active TSS	Pancreas	Pancrea
44	chr19:39109200-39110400	Active TSS	Right Ventricle	heart
45	chr19:39109200-39110400	Active TSS	Spleen	Spleen
46	chr19:39109200-39110400	Active TSS	Hela-S3	cervix
47	chr19:39109200-39110400	Active TSS	NHDF-Ad	bronchial
48	chr19:39109200-39110600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr19:39109200-39110600	Active TSS	H9 Cell Line	embryonic stem cell
50	chr19:39109200-39110600	Active TSS	HUES6 Cell Line	embryonic stem cell

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