Variant report

Variant	rs532982602
Chromosome Location	chr19:56186005-56186006
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	POLR2A	chr19:56185989-56187017	MCF-7	breast:	n/a	n/a
2	MAZ	chr19:56185625-56187879	IMR90	lung:	n/a	n/a
3	POLR2A	chr19:56185886-56187058	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:56184849-56186152	HL-60	blood:	n/a	n/a
5	GABPA	chr19:56185875-56187128	K562	blood:	n/a	chr19:56186319-56186328 chr19:56186566-56186573 chr19:56186868-56186877
6	POLR2A	chr19:56185595-56187287	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:56185967-56187116	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:56185604-56186939	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:56185589-56187693	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:56185658-56187111	Hela-S3	cervix:	n/a	n/a
11	SIX5	chr19:56185991-56186729	A549	lung:	n/a	n/a
12	TCF12	chr19:56185766-56187007	A549	lung:	n/a	n/a
13	HCFC1	chr19:56185639-56187350	Hela-S3	cervix:	n/a	n/a
14	SP1	chr19:56185489-56186102	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:56185652-56187179	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr19:56185613-56187158	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:56185739-56187205	A549	lung:	n/a	n/a
18	POLR2A	chr19:56185507-56187227	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:56185861-56187037	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr19:56185664-56187793	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr19:56185656-56186978	Hela-S3	cervix:	n/a	n/a
22	GABPA	chr19:56185814-56187449	A549	lung:	n/a	chr19:56186319-56186328 chr19:56186566-56186573 chr19:56186868-56186877
23	POLR2A	chr19:56185622-56187312	K562	blood:	n/a	n/a
24	ELF1	chr19:56186001-56187079	GM12878	blood:	n/a	chr19:56186776-56186788 chr19:56186813-56186825 chr19:56186323-56186335
25	POLR2A	chr19:56185938-56187074	GM12891	blood:	n/a	n/a
26	POLR2A	chr19:56185621-56187334	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:56185523-56187118	K562	blood:	n/a	n/a
28	POLR2A	chr19:56185983-56186806	U87	brain:	n/a	n/a
29	POLR2A	chr19:56185833-56187056	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:56185987-56186812	U87	brain:	n/a	n/a
31	POLR2A	chr19:56185716-56186997	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:56185645-56187033	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr19:56185570-56187206	GM12892	blood:	n/a	n/a
34	POLR2A	chr19:56185699-56186763	HepG2	liver:	n/a	n/a
35	POLR2A	chr19:56185761-56187676	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:56185541-56187012	GM12892	blood:	n/a	n/a
37	MXI1	chr19:56185791-56188335	SK-N-SH	brain:	n/a	n/a
38	REST	chr19:56185572-56186047	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr19:56185988-56187218	GM18505	blood:	n/a	n/a
40	POLR2A	chr19:56185621-56186813	K562	blood:	n/a	n/a
41	POLR2A	chr19:56185977-56186806	GM12891	blood:	n/a	n/a
42	POLR2A	chr19:56185745-56187135	GM19193	blood:	n/a	n/a
43	POLR2A	chr19:56185517-56186989	K562	blood:	n/a	n/a
44	POLR2A	chr19:56185652-56187081	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr19:56185610-56187159	PFSK-1	brain:	n/a	n/a
46	BCL3	chr19:56185716-56186845	A549	lung:	n/a	chr19:56186662-56186671 chr19:56186569-56186578 chr19:56186659-56186668 chr19:56186810-56186819 chr19:56186433-56186442 chr19:56186182-56186195 chr19:56186420-56186433 chr19:56186475-56186484 chr19:56186189-56186202 chr19:56186657-56186670
47	POLR2A	chr19:56185687-56186865	K562	blood:	n/a	n/a
48	POLR2A	chr19:56185740-56186093	K562	blood:	n/a	n/a
49	POLR2A	chr19:56185991-56186845	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
2	chr19:56185642..56190165-chr19:56193908..56196750,4	MCF-7	breast:
3	chr19:56185115..56186636-chr21:46236479..46238156,2	MCF-7	breast:
4	chr19:55986321..55989143-chr19:56184299..56186966,2	K562	blood:
5	chr19:56114907..56116947-chr19:56184542..56187154,2	K562	blood:
6	chr19:56158129..56161096-chr19:56185326..56187791,3	MCF-7	breast:

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000184900	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000211571	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000197483	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription 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	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv3406564	chr19:56184365-56186913	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv3337861	chr19:56185190-56186188	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv522559	chr19:56185250-56190815	Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56182400-56186200	Weak transcription	Aorta	Aorta
2	chr19:56183000-56186200	Weak transcription	Small Intestine	intestine
3	chr19:56183200-56186200	Weak transcription	Gastric	stomach
4	chr19:56183200-56186200	Weak transcription	Pancreas	Pancrea
5	chr19:56185000-56186800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:56185200-56187600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:56185200-56187800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:56185400-56187400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr19:56185400-56187400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:56185400-56187400	Active TSS	K562	blood
11	chr19:56185400-56188000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:56185400-56188000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:56185600-56186200	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
14	chr19:56185600-56186200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:56185600-56186200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:56185600-56186200	Flanking Active TSS	Hela-S3	cervix
17	chr19:56185600-56186400	Enhancers	Primary hematopoietic stem cells	blood
18	chr19:56185600-56187600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr19:56185600-56187600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:56185600-56188000	Active TSS	HSMM	muscle
21	chr19:56185800-56186200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:56185800-56186200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr19:56185800-56186200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr19:56185800-56186200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:56185800-56186200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:56185800-56186200	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr19:56185800-56186200	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr19:56185800-56186200	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr19:56185800-56186200	Weak transcription	Esophagus	oesophagus
30	chr19:56185800-56186200	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
31	chr19:56185800-56186200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
32	chr19:56185800-56186200	Flanking Active TSS	Right Ventricle	heart
33	chr19:56185800-56186200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr19:56185800-56186200	Flanking Active TSS	NHEK	skin
35	chr19:56185800-56186400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr19:56185800-56186400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:56185800-56186400	Flanking Active TSS	Liver	Liver
38	chr19:56185800-56186400	Enhancers	Fetal Brain Male	brain
39	chr19:56185800-56186600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:56185800-56186600	Enhancers	Spleen	Spleen
41	chr19:56185800-56187200	Active TSS	H1 Cell Line	embryonic stem cell
42	chr19:56185800-56187400	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:56185800-56187400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:56185800-56187600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:56185800-56187800	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr19:56185800-56187800	Active TSS	Psoas Muscle	Psoas
47	chr19:56185800-56187800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr19:56186000-56186200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:56186000-56186200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:56186000-56186200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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