Variant report

Variant	rs2232988
Chromosome Location	chr19:39109117-39109118
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	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
3	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
4	GTF2F1	chr19:39108993-39109984	H1-hESC	embryonic stem cell:	n/a	n/a
5	RUNX3	chr19:39107907-39110161	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:39108832-39109204	GM12891	blood:	n/a	n/a
7	RELA	chr19:39108050-39110036	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:39108374-39109607	GM12892	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	POLR2A	chr19:39108990-39110165	HUVEC	blood vessel:	n/a	n/a
12	BCLAF1	chr19:39108124-39109266	GM12878	blood:	n/a	chr19:39108867-39108876
13	POLR2A	chr19:39107935-39110102	GM12878	blood:	n/a	n/a
14	TCF12	chr19:39108662-39110703	A549	lung:	n/a	chr19:39110689-39110696
15	ZEB1	chr19:39108483-39109607	GM12878	blood:	n/a	n/a
16	SIX5	chr19:39108632-39110279	A549	lung:	n/a	n/a
17	SIX5	chr19:39108964-39110077	A549	lung:	n/a	n/a
18	POLR2A	chr19:39108098-39110085	GM15510	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	EP300	chr19:39108886-39110695	A549	lung:	n/a	n/a
22	MAX	chr19:39108997-39109955	H1-hESC	embryonic stem cell:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39109718-39109737 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
23	CTCF	chr19:39109041-39109136	Lung_OC	lung:	n/a	n/a
24	POLR2A	chr19:39108805-39110710	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:39108977-39110037	HCT-116	colon:	n/a	n/a
26	POLR2A	chr19:39108920-39110060	HEK293	kidney:	n/a	n/a
27	POLR2A	chr19:39108499-39110186	HL-60	blood:	n/a	n/a
28	POLR2A	chr19:39108908-39110076	K562	blood:	n/a	n/a
29	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
30	POLR2A	chr19:39107886-39110202	GM12892	blood:	n/a	n/a
31	SIN3A	chr19:39108125-39110525	GM12878	blood:	n/a	chr19:39109722-39109731 chr19:39109309-39109318 chr19:39110041-39110055
32	POLR2A	chr19:39107795-39111328	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr19:39108443-39111312	PANC-1	pancreas:	n/a	n/a
34	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
35	RELA	chr19:39108456-39109162	GM18526	blood:	n/a	n/a
36	POLR2A	chr19:39108040-39109165	GM12878	blood:	n/a	n/a
37	USF2	chr19:39109022-39109952	GM12878	blood:	n/a	chr19:39109721-39109734 chr19:39109721-39109732
38	POLR2A	chr19:39107997-39110181	GM12878	blood:	n/a	n/a
39	RELA	chr19:39108007-39110024	GM19193	blood:	n/a	n/a
40	POLR2A	chr19:39108007-39110122	Raji	blood:	n/a	n/a
41	SP1	chr19:39109104-39110154	A549	lung:	n/a	chr19:39109601-39109613 chr19:39109603-39109612 chr19:39109602-39109612 chr19:39109602-39109616 chr19:39109602-39109611 chr19:39109602-39109611 chr19:39109602-39109612 chr19:39109601-39109613
42	BCL3	chr19:39108731-39110848	A549	lung:	n/a	chr19:39109262-39109275 chr19:39110004-39110013 chr19:39109603-39109616 chr19:39110055-39110068 chr19:39108867-39108876
43	REST	chr19:39108965-39110148	A549	lung:	n/a	chr19:39109783-39109791
44	GABPA	chr19:39108902-39110657	A549	lung:	n/a	chr19:39109690-39109701 chr19:39109626-39109635 chr19:39109023-39109034 chr19:39109023-39109032 chr19:39109624-39109638 chr19:39109020-39109034 chr19:39109687-39109701 chr19:39109690-39109699 chr19:39109624-39109635 chr19:39109603-39109612
45	POLR2A	chr19:39108769-39110216	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr19:39108946-39110097	K562	blood:	n/a	n/a
47	RCOR1	chr19:39108060-39110038	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:39108158-39113791	PANC-1	pancreas:	n/a	n/a
49	CHD2	chr19:39108429-39109972	GM12878	blood:	n/a	n/a
50	RELA	chr19:39108010-39110032	GM15510	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39109076-39109126	GM19239	blood:	n/a
2	chr19:39109076-39109126	HRCEpiC	kidney:	n/a
3	chr19:39109076-39109126	MCF-7	breast:	n/a
4	chr19:39109076-39109126	PrEC	prostate:	n/a
5	chr19:39109076-39109126	AG10803	skin:	n/a
6	chr19:39109076-39109126	Caco-2	colon:	n/a
7	chr19:39109076-39109126	NH-A	brain:	n/a
8	chr19:39109076-39109126	GM12892	blood:	n/a
9	chr19:39109076-39109126	HUVEC	blood vessel:	n/a
10	chr19:39109076-39109126	NHDF-neo	bronchial:	n/a
11	chr19:39109076-39109126	PFSK-1	brain:	n/a
12	chr19:39109076-39109126	ProgFib	skin:	n/a
13	chr19:39109076-39109126	HIPEpiC	eye:	n/a
14	chr19:39109076-39109126	NT2-D1	testis:	n/a
15	chr19:39109076-39109126	PANC-1	pancreas:	n/a
16	chr19:39109076-39109126	HMEC	breast:	n/a
17	chr19:39109076-39109126	HCPEpiC	choroid plexus:	n/a
18	chr19:39109076-39109126	Hepatocyte	liver:	n/a
19	chr19:39109076-39109126	H1-hESC	embryonic stem cell:	embryo
20	chr19:39109076-39109126	BJ	skin:	n/a
21	chr19:39109076-39109126	HRPEpiC	eye:	n/a
22	chr19:39109076-39109126	A549	lung:	n/a
23	chr19:39109076-39109126	AG09319	gingival:	n/a
24	chr19:39109076-39109126	HepG2	liver:	n/a
25	chr19:39109076-39109126	T-47D	breast:	n/a
26	chr19:39109076-39109126	BE2_C	brain:	n/a
27	chr19:39109076-39109126	CMK	blood:	n/a
28	chr19:39109076-39109126	IMR90	lung:	fetal
29	chr19:39109076-39109126	ovcar-3	ovarian:	n/a
30	chr19:39109076-39109126	AG04450	lung:	fetal
31	chr19:39109076-39109126	AG04449	skin:	fetal
32	chr19:39109076-39109126	MCF10A-Er-Src	breast:	n/a
33	chr19:39109076-39109126	GM12891	blood:	n/a
34	chr19:39109076-39109126	SKMC	muscle:	n/a
35	chr19:39109076-39109126	SK-N-SH	brain:	n/a
36	chr19:39109076-39109126	HPAEpiC	pulmonary alveolar:	n/a
37	chr19:39109076-39109126	SK-N-MC	brain:	n/a
38	chr19:39109076-39109126	LNCaP	prostate:	n/a
39	chr19:39109076-39109126	AG09309	skin:	n/a
40	chr19:39109076-39109126	NB4	blood:	n/a
41	chr19:39109076-39109126	HL-60	blood:	n/a
42	chr19:39109076-39109126	SK-N-SH_RA	brain:	n/a
43	chr19:39109076-39109126	HAEpiC	amniotic membrane:	n/a
44	chr19:39109076-39109126	AoSMC	blood vessel:	n/a
45	chr19:39109076-39109126	HEEpiC	esophagus:	n/a
46	chr19:39109076-39109126	HEK293	kidney:	embryo
47	chr19:39109076-39109126	U87	brain:	n/a
48	chr19:39109076-39109126	RPTEC	kidney:	n/a
49	chr19:39109076-39109126	GM06990	blood:	n/a
50	chr19:39109076-39109126	Jurkat	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	chr19:39109034..39110948-chr19:39138125..39139962,2	MCF-7	breast:
6	chr19:39103433..39106687-chr19:39106977..39109796,8	K562	blood:
7	chr19:39107241..39111219-chr19:39136508..39140596,7	K562	blood:
8	chr19:39102966..39104689-chr19:39107783..39109776,2	MCF-7	breast:
9	chr19:39108057..39110372-chr19:39339414..39342268,3	K562	blood:
10	chr19:39024830..39027065-chr19:39108421..39111246,2	MCF-7	breast:
11	chr19:39103495..39106423-chr19:39106849..39111061,4	MCF-7	breast:
12	chr19:39101758..39105983-chr19:39106668..39109959,5	K562	blood:
13	chr19:39108167..39112213-chr19:39136508..39140596,7	K562	blood:
14	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
ENSG00000130402	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000267291	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs8112979	1.00[YRI][hapmap];0.86[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39106800-39109600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
2	chr19:39107000-39109200	Flanking Active TSS	Dnd41	blood
3	chr19:39107000-39109400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr19:39107000-39109600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr19:39107200-39109400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:39107200-39109600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr19:39107600-39110200	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr19:39107800-39109400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr19:39107800-39109400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr19:39107800-39110600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:39107800-39111000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:39108000-39109400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr19:39108000-39109400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr19:39108000-39109400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:39108000-39109400	Flanking Active TSS	Fetal Thymus	thymus
16	chr19:39108000-39109600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr19:39108000-39109600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:39108000-39110200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:39108200-39109400	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr19:39108200-39109600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr19:39108400-39109200	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr19:39108400-39109200	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr19:39108400-39109200	Flanking Active TSS	Esophagus	oesophagus
24	chr19:39108400-39109200	Flanking Active TSS	Right Ventricle	heart
25	chr19:39108400-39109400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr19:39108400-39109400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr19:39108400-39109400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:39108400-39109400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr19:39108400-39109400	Flanking Active TSS	Placenta	Placenta
30	chr19:39108400-39109400	Flanking Active TSS	K562	blood
31	chr19:39108400-39110400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr19:39108400-39110400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:39108400-39110600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr19:39108400-39111000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr19:39108600-39109200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:39108600-39109200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr19:39108600-39109200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr19:39108600-39109200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:39108600-39109200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr19:39108600-39109200	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr19:39108600-39109200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr19:39108600-39109200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:39108600-39109200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr19:39108600-39109400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:39108600-39109400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:39108600-39109400	Flanking Active TSS	Colonic Mucosa	Colon
47	chr19:39108600-39109400	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr19:39108600-39109400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr19:39108600-39109400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr19:39108600-39109400	Flanking Active TSS	GM12878-XiMat	blood

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