Variant report

Variant	rs73038936
Chromosome Location	chr19:39210733-39210734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr19:39210398-39211511	ECC-1	luminal epithelium:	n/a	chr19:39211104-39211114
2	REST	chr19:39210708-39211441	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39209151-39211490	K562	blood:	n/a	n/a
4	POLR2A	chr19:39209094-39212892	U87	brain:	n/a	n/a
5	POLR2A	chr19:39208578-39211524	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:39210420-39211075	A549	lung:	n/a	n/a
7	MAX	chr19:39209756-39210969	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr19:39208997-39211919	K562	blood:	n/a	n/a
9	POLR2A	chr19:39209073-39214530	K562	blood:	n/a	n/a
10	POLR2A	chr19:39210502-39210791	Hela-S3	cervix:	n/a	n/a
11	NFIC	chr19:39209743-39211373	ECC-1	luminal epithelium:	n/a	chr19:39210932-39210949
12	POLR2A	chr19:39209212-39215383	A549	lung:	n/a	n/a
13	POLR2A	chr19:39210615-39210880	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:39210641-39211145	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:39210628-39210877	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr19:39210446-39211025	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:39210588-39210989	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:39210707-39211134	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:39209202-39214711	K562	blood:	n/a	n/a
20	SIN3AK20	chr19:39209168-39211446	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr19:39210639-39211345	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZBTB7A	chr19:39209161-39211258	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr19:39206681-39226302	PANC-1	pancreas:	n/a	n/a
24	NFIC	chr19:39210597-39211426	ECC-1	luminal epithelium:	n/a	chr19:39210932-39210949
25	POLR2A	chr19:39209161-39211240	HL-60	blood:	n/a	n/a
26	POLR2A	chr19:39210144-39210800	K562	blood:	n/a	n/a
27	ZBTB7A	chr19:39210166-39211208	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr19:39210467-39212805	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr19:39210379-39211569	A549	lung:	n/a	n/a
30	POLR2A	chr19:39209088-39212955	U87	brain:	n/a	n/a
31	POLR2A	chr19:39209732-39211522	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr19:39206712-39220782	PANC-1	pancreas:	n/a	n/a
33	BCL3	chr19:39210019-39211336	A549	lung:	n/a	n/a
34	EP300	chr19:39209651-39211562	ECC-1	luminal epithelium:	n/a	chr19:39210830-39210846

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39209590..39213111-chr19:39330256..39333147,3	MCF-7	breast:
2	chr19:39138734..39141158-chr19:39210569..39212913,2	MCF-7	breast:
3	chr19:39141347..39144030-chr19:39208371..39211834,3	MCF-7	breast:
4	chr19:39210151..39212274-chr19:39220710..39223551,2	MCF-7	breast:
5	chr19:39210554..39212101-chr19:39326682..39329322,2	MCF-7	breast:
6	chr19:39210217..39211879-chr19:39211993..39213574,2	MCF-7	breast:
7	chr19:39207862..39211804-chr19:39330654..39334530,3	MCF-7	breast:
8	chr19:39196541..39198571-chr19:39208360..39211296,2	K562	blood:
9	chr19:39151274..39153019-chr19:39209216..39212183,2	MCF-7	breast:
10	chr19:39209335..39212067-chr19:39340006..39342990,3	MCF-7	breast:
11	chr19:39138189..39142372-chr19:39210085..39214804,5	MCF-7	breast:

No data

Variant related genes	Relation type
ACTN4	TF binding region
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11553600	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052046	1.00[ASN][1000 genomes]
rs17589415	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17665451	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41482151	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45468197	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4802744	1.00[ASN][1000 genomes]
rs4802747	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802775	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67438539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67953948	1.00[ASN][1000 genomes]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	1.00[ASN][1000 genomes]
rs73032691	1.00[ASN][1000 genomes]
rs73032697	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034621	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038909	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038918	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038932	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73038948	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7351086	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103824	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182484	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888995	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39186400-39213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:39189400-39223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:39189800-39222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39190000-39218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:39190200-39222600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr19:39190200-39222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:39190400-39212000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:39190400-39212200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:39190400-39217000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:39190400-39218000	Strong transcription	Primary T cells from cord blood	blood
13	chr19:39190400-39222400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:39190400-39222600	Strong transcription	Dnd41	blood
15	chr19:39190600-39216400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr19:39190600-39217000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:39190600-39219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:39190600-39222800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:39190800-39220400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:39190800-39222600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr19:39190800-39222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:39190800-39222800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr19:39190800-39223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:39190800-39223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:39191000-39222400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:39191000-39222600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr19:39191400-39218800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:39192400-39221200	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:39199000-39215600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:39199000-39220400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr19:39199400-39215400	Weak transcription	Fetal Kidney	kidney
32	chr19:39199800-39214600	Strong transcription	HUVEC	blood vessel
33	chr19:39200400-39217200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr19:39202800-39221400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:39203400-39218600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:39204200-39223400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr19:39204600-39211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:39205000-39221000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:39205400-39211600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:39205600-39212200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr19:39205800-39211600	Weak transcription	Hela-S3	cervix
42	chr19:39205800-39212600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:39206800-39214200	Genic enhancers	Left Ventricle	heart
44	chr19:39206800-39220000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr19:39206800-39220000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:39207000-39212200	Strong transcription	Aorta	Aorta
47	chr19:39207000-39213600	Genic enhancers	Pancreas	Pancrea
48	chr19:39207000-39214800	Genic enhancers	Right Ventricle	heart
49	chr19:39207000-39219400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr19:39207000-39220200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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