Variant report

Variant	rs12981254
Chromosome Location	chr19:51849927-51849928
allele	C/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	chr19:51845282-51851367	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:51841814-51851408	HepG2	liver:	n/a	n/a
3	CTCF	chr19:51849875-51850253	H1-hESC	embryonic stem cell:	n/a	chr19:51850079-51850095 chr19:51850078-51850096 chr19:51850081-51850090 chr19:51850081-51850094
4	POLR2A	chr19:51849781-51850665	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:51849479-51851373	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:51849885-51850384	K562	blood:	n/a	n/a
7	POLR2A	chr19:51849831-51850645	HepG2	liver:	n/a	n/a
8	CTCF	chr19:51849900-51850050	HCT-116	colon:	n/a	n/a
9	CTCF	chr19:51849913-51850239	H1-hESC	embryonic stem cell:	n/a	chr19:51850079-51850095 chr19:51850078-51850096 chr19:51850081-51850090 chr19:51850081-51850094
10	HEY1	chr19:51849747-51851272	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:51849809-51851322	K562	blood:	n/a	n/a
12	POLR2A	chr19:51844742-51856690	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:51849684-51850358	K562	blood:	n/a	n/a
14	RAD21	chr19:51849909-51850304	H1-hESC	embryonic stem cell:	n/a	chr19:51850129-51850141 chr19:51850079-51850098 chr19:51850084-51850096
15	POLR2A	chr19:51849293-51851365	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:51848871..51850379-chr19:51869633..51872524,2	MCF-7	breast:
2	chr19:51848237..51856350-chr19:51866106..51872931,10	MCF-7	breast:

Variant related genes	Relation type
VSIG10L	TF binding region
ENSG00000105379	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000160318	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12975011	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976097	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12977906	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12979526	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2411326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59890391	0.91[EUR][1000 genomes]
rs8102334	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8102664	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8107232	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107235	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107468	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1813225	chr19:51821612-51888813	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv912294	chr19:51844978-51878841	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers 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	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51843000-51852200	Weak transcription	Fetal Heart	heart
2	chr19:51843000-51857600	Weak transcription	Fetal Kidney	kidney
3	chr19:51843200-51857400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:51843600-51854000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:51843800-51854400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:51843800-51857600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:51844000-51850000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:51844000-51850200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:51844000-51851800	Weak transcription	HSMM	muscle
10	chr19:51844000-51852000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:51844000-51857400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:51844000-51865800	Weak transcription	Small Intestine	intestine
13	chr19:51844000-51866400	Weak transcription	Right Atrium	heart
14	chr19:51844200-51853400	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:51844200-51854200	Weak transcription	Psoas Muscle	Psoas
16	chr19:51844200-51857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:51844200-51857600	Weak transcription	NH-A	brain
18	chr19:51845800-51856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:51846000-51857600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:51846200-51852800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:51846200-51856400	Weak transcription	Fetal Brain Male	brain
22	chr19:51846200-51857400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr19:51846200-51857600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:51846400-51854200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:51846400-51857200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:51846400-51857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:51846400-51857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:51846400-51857400	Weak transcription	Stomach Mucosa	stomach
29	chr19:51846600-51855600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr19:51846600-51857400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:51846600-51857600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr19:51847000-51851000	Strong transcription	Fetal Intestine Small	intestine
33	chr19:51847200-51851200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:51847200-51851200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:51847200-51856600	Strong transcription	Fetal Stomach	stomach
36	chr19:51847200-51868600	Weak transcription	Fetal Lung	lung
37	chr19:51847400-51850600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:51847400-51851200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:51847400-51851200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:51847400-51851200	Strong transcription	Thymus	Thymus
41	chr19:51847400-51851200	Strong transcription	Dnd41	blood
42	chr19:51847400-51851400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:51847400-51851400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr19:51847400-51851800	Strong transcription	Left Ventricle	heart
45	chr19:51847400-51856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:51847400-51856600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr19:51847400-51858200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr19:51847600-51856600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:51847800-51851000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:51847800-51851200	Strong transcription	Spleen	Spleen

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