Variant report

Variant	rs17884899
Chromosome Location	chr19:39899328-39899329
allele	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	POLR2A	chr19:39898986-39905074	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF2	chr19:39899263-39899720	K562	blood:	n/a	n/a
3	SIN3AK20	chr19:39895490-39907815	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39896853-39907805	IMR90	lung:	n/a	n/a
5	POLR2A	chr19:39896847-39904491	U87	brain:	n/a	n/a
6	POLR2A	chr19:39897070-39899594	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr19:39896816-39903789	HCT-116	colon:	n/a	n/a
8	POLR2A	chr19:39896917-39899899	K562	blood:	n/a	n/a
9	POLR2A	chr19:39897307-39904232	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:39896830-39899884	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:39896730-39901249	K562	blood:	n/a	n/a
12	POLR2A	chr19:39896827-39903535	HCT-116	colon:	n/a	n/a
13	POLR2A	chr19:39896460-39903920	MCF10A-Er-Src	breast:	n/a	n/a
14	JUND	chr19:39897180-39903728	HCT-116	colon:	n/a	chr19:39903202-39903211 chr19:39900169-39900178
15	PML	chr19:39896851-39901510	GM12878	blood:	n/a	n/a
16	PML	chr19:39899294-39901100	K562	blood:	n/a	n/a
17	POLR2A	chr19:39897258-39899913	GM12892	blood:	n/a	n/a
18	POLR2A	chr19:39897208-39903534	K562	blood:	n/a	n/a
19	POLR2A	chr19:39897033-39901180	MCF-7	breast:	n/a	n/a
20	ELF1	chr19:39899323-39899851	A549	lung:	n/a	n/a
21	POLR2A	chr19:39897175-39899869	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:39899327-39899926	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:39896863-39901096	GM15510	blood:	n/a	n/a
24	ETS1	chr19:39897412-39899387	K562	blood:	n/a	chr19:39897855-39897865 chr19:39897854-39897863
25	POLR2A	chr19:39896847-39904730	U87	brain:	n/a	n/a
26	POLR2A	chr19:39897402-39901552	K562	blood:	n/a	n/a
27	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
28	MAZ	chr19:39896170-39907106	IMR90	lung:	n/a	chr19:39902942-39902955 chr19:39903201-39903211 chr19:39906097-39906107 chr19:39900090-39900100 chr19:39897711-39897721 chr19:39902944-39902953 chr19:39902944-39902953 chr19:39902942-39902955 chr19:39902942-39902955 chr19:39903336-39903345 chr19:39903271-39903281 chr19:39904354-39904364 chr19:39904055-39904065 chr19:39904327-39904337 chr19:39904845-39904855 chr19:39902943-39902954
29	POLR2A	chr19:39896839-39899872	GM12892	blood:	n/a	n/a
30	USF2	chr19:39897428-39900958	GM12878	blood:	n/a	n/a
31	CUX1	chr19:39899251-39901028	GM12878	blood:	n/a	n/a
32	CEBPD	chr19:39897129-39903693	K562	blood:	n/a	chr19:39898047-39898058
33	BCLAF1	chr19:39897427-39903224	K562	blood:	n/a	chr19:39897575-39897588 chr19:39903202-39903215 chr19:39900162-39900171 chr19:39897854-39897863 chr19:39900810-39900823
34	POLR2A	chr19:39897103-39902437	ProgFib	skin:	n/a	n/a
35	HEY1	chr19:39897296-39899853	K562	blood:	n/a	chr19:39897370-39897385 chr19:39897491-39897500
36	MTA3	chr19:39896751-39905454	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:39896979-39899816	A549	lung:	n/a	n/a
38	POLR2A	chr19:39898245-39900933	U87	brain:	n/a	n/a
39	POLR2A	chr19:39896847-39901505	HCT-116	colon:	n/a	n/a
40	NFATC1	chr19:39898963-39901172	GM12878	blood:	n/a	n/a
41	TAF1	chr19:39898395-39899836	K562	blood:	n/a	n/a
42	POLR2A	chr19:39898245-39900960	U87	brain:	n/a	n/a
43	SIN3AK20	chr19:39899085-39899852	K562	blood:	n/a	n/a
44	PBX3	chr19:39898249-39899955	A549	lung:	n/a	n/a
45	POLR2A	chr19:39896846-39899865	HL-60	blood:	n/a	n/a
46	TCF7L2	chr19:39898366-39899792	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr19:39896685-39904546	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:39897032-39903757	GM12878	blood:	n/a	n/a
49	MAX	chr19:39896069-39899908	A549	lung:	n/a	chr19:39897711-39897721
50	POLR2A	chr19:39897140-39907785	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39420462..39423214-chr19:39898290..39900735,2	K562	blood:
2	chr17:76309600..76310588-chr19:39899296..39900165,2	Hela-S3	cervix:
3	chr19:39615191..39619693-chr19:39896201..39900336,5	K562	blood:
4	chr19:39899305..39899968-chr3:196594275..196595222,2	Hela-S3	cervix:
5	chr19:39657697..39659384-chr19:39897167..39900031,2	MCF-7	breast:
6	chr19:39898640..39900302-chr19:40323099..40324654,2	K562	blood:
7	chr19:39898615..39903463-chr19:40021264..40024360,6	K562	blood:
8	chr19:39899240..39899968-chrX:118108903..118109791,2	Hela-S3	cervix:
9	chr19:39898397..39900372-chr19:40006194..40008008,2	K562	blood:
10	chr19:39897603..39899385-chr19:39988618..39990162,2	K562	blood:
11	chr19:39420323..39422094-chr19:39898290..39901814,3	K562	blood:
12	chr19:39831462..39833819-chr19:39895852..39900331,6	MCF-7	breast:
13	chr19:19496705..19497612-chr19:39898856..39899619,2	Hela-S3	cervix:
14	chr11:122932621..122933140-chr19:39899305..39900038,2	Hela-S3	cervix:
15	chr19:39694375..39697008-chr19:39898075..39900660,3	MCF-7	breast:
16	chr16:87425513..87426350-chr19:39899091..39899952,2	Hela-S3	cervix:
17	chr19:39846643..39848442-chr19:39897327..39899339,2	MCF-7	breast:
18	chr1:45987463..45988268-chr19:39899150..39899825,2	Hela-S3	cervix:
19	chr19:39898615..39904728-chr19:40019936..40025504,8	K562	blood:
20	chr19:39830669..39836861-chr19:39895802..39900887,6	MCF-7	breast:
21	chr19:39899289..39900139-chr8:134584456..134584993,2	Hela-S3	cervix:
22	chr14:60715484..60716055-chr19:39899068..39899945,2	Hela-S3	cervix:
23	chr12:10873260..10876044-chr19:39898902..39901663,2	K562	blood:
24	chr15:51055767..51057855-chr19:39899197..39901640,2	MCF-7	breast:
25	chr19:39898553..39902206-chr19:39948362..39950815,3	K562	blood:
26	chr19:39828912..39834348-chr19:39896525..39904623,14	K562	blood:
27	chr17:56708804..56709573-chr19:39899089..39900014,2	Hela-S3	cervix:

Variant related genes	Relation type
PLEKHG2	TF binding region
ENSG00000140941	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000103264	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000175556	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000100614	Chromatin interaction
ENSG00000109971	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000186838	Chromatin interaction
ENSG00000060138	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000119231	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000138600	Chromatin interaction
ENSG00000179751	Chromatin interaction
ENSG00000179134	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2233711	1.00[CHB][hapmap]
rs2304218	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active 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 miRNA target site	222 gene(s)	inside rSNPs	diseases
9	nsv911686	chr19:39891219-39907781	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
10	nsv911687	chr19:39891219-39909714	Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
11	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39896600-39901400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr19:39896600-39901600	Active TSS	Psoas Muscle	Psoas
3	chr19:39896800-39899400	Active TSS	Brain Angular Gyrus	brain
4	chr19:39896800-39899400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr19:39896800-39900000	Active TSS	Right Atrium	heart
6	chr19:39897000-39899800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:39897000-39900600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39897000-39900800	Active TSS	Liver	Liver
9	chr19:39897000-39901000	Active TSS	Fetal Kidney	kidney
10	chr19:39897000-39901000	Active TSS	Ovary	ovary
11	chr19:39897000-39901200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:39897200-39899400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:39897200-39899400	Active TSS	HSMMtube	muscle
14	chr19:39897200-39900000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
15	chr19:39897400-39899600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
16	chr19:39897600-39899600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
17	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
18	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
22	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
23	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
24	chr19:39897600-39899800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
25	chr19:39897600-39899800	Transcr. at gene 5' and 3'	NHEK	skin
26	chr19:39897600-39900200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:39897600-39900200	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
28	chr19:39897600-39900200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
29	chr19:39897600-39901600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:39897800-39899800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
31	chr19:39897800-39899800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
32	chr19:39897800-39899800	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
33	chr19:39897800-39899800	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
34	chr19:39898000-39899600	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
35	chr19:39898000-39899600	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
36	chr19:39898000-39899800	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
37	chr19:39898000-39899800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
38	chr19:39898000-39899800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:39898000-39899800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
40	chr19:39898000-39899800	Transcr. at gene 5' and 3'	NHLF	lung
41	chr19:39898200-39899600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:39898200-39899600	Transcr. at gene 5' and 3'	Sigmoid Colon	Sigmoid Colon
43	chr19:39898200-39899800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:39898200-39899800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
45	chr19:39898200-39900000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
46	chr19:39898200-39900200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:39898200-39900200	Transcr. at gene 5' and 3'	Thymus	Thymus
48	chr19:39898400-39899400	Transcr. at gene 5' and 3'	Aorta	Aorta
49	chr19:39898400-39899400	Transcr. at gene 5' and 3'	Pancreatic Islets	Pancreatic Islet
50	chr19:39898400-39899600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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