Variant report

Variant	rs61496908
Chromosome Location	chr19:38397575-38397576
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	TCF7L2	chr19:38397244-38398080	HCT-116	colon:	n/a	n/a
2	TAF1	chr19:38396940-38398238	H1-neurons	neurons:	n/a	n/a
3	E2F4	chr19:38397561-38397927	GM12878	blood:	n/a	chr19:38397794-38397804 chr19:38397864-38397875
4	POLR2A	chr19:38396994-38398157	GM19099	blood:	n/a	n/a
5	ZNF143	chr19:38397488-38398786	Hela-S3	cervix:	n/a	chr19:38397847-38397856 chr19:38397748-38397766 chr19:38397781-38397799 chr19:38397845-38397863 chr19:38397845-38397854 chr19:38397794-38397804
6	E2F6	chr19:38396670-38397732	H1-hESC	embryonic stem cell:	n/a	chr19:38397674-38397685 chr19:38397430-38397439
7	POLR2A	chr19:38396886-38398186	MCF-7	breast:	n/a	n/a
8	MXI1	chr19:38396701-38398350	HepG2	liver:	n/a	n/a
9	HMGN3	chr19:38397047-38398303	K562	blood:	n/a	n/a
10	CTCF	chr19:38397400-38397690	HEEpiC	esophagus:	n/a	chr19:38397467-38397480
11	CTCF	chr19:38397500-38397650	HCM	heart:	n/a	n/a
12	ATF3	chr19:38397218-38398111	A549	lung:	n/a	n/a
13	PAX5	chr19:38397073-38398331	GM12892	blood:	n/a	chr19:38397430-38397439 chr19:38397894-38397904
14	PAX5	chr19:38397545-38397919	GM12878	blood:	n/a	chr19:38397894-38397904
15	GABPA	chr19:38397548-38397974	H1-hESC	embryonic stem cell:	n/a	chr19:38397799-38397808
16	POLR2A	chr19:38397370-38398209	A549	lung:	n/a	n/a
17	ELF1	chr19:38397393-38398188	SK-N-SH	brain:	n/a	chr19:38398119-38398131 chr19:38398115-38398124 chr19:38397465-38397477 chr19:38397698-38397711
18	POLR2A	chr19:38397546-38398278	Hela-S3	cervix:	n/a	n/a
19	YY1	chr19:38397557-38398102	ECC-1	luminal epithelium:	n/a	chr19:38397790-38397801
20	MAZ	chr19:38396965-38398172	HepG2	liver:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
21	CTCF	chr19:38397480-38397630	AG10803	skin:	n/a	n/a
22	MAZ	chr19:38396945-38398347	IMR90	lung:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
23	ZBTB33	chr19:38397392-38398108	A549	lung:	n/a	chr19:38397797-38397807 chr19:38397967-38397977
24	MAX	chr19:38396600-38398287	NB4	blood:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
25	YY1	chr19:38397482-38398075	SK-N-SH_RA	brain:	n/a	chr19:38397790-38397801
26	YY1	chr19:38397508-38398092	GM12891	blood:	n/a	chr19:38397790-38397801
27	GATA3	chr19:38396587-38397823	MCF-7	breast:	n/a	n/a
28	SPI1	chr19:38397539-38397981	GM12891	blood:	n/a	n/a
29	YY1	chr19:38397527-38398058	K562	blood:	n/a	chr19:38397790-38397801
30	ELK1	chr19:38397383-38398143	GM12878	blood:	n/a	n/a
31	MYC	chr19:38396948-38398019	K562	blood:	n/a	chr19:38397081-38397090 chr19:38397082-38397089
32	MXI1	chr19:38396961-38398476	H1-hESC	embryonic stem cell:	n/a	n/a
33	RELA	chr19:38397063-38398062	GM18951	blood:	n/a	n/a
34	TAF1	chr19:38396757-38398154	H1-hESC	embryonic stem cell:	n/a	n/a
35	ZEB1	chr19:38396873-38397895	GM12878	blood:	n/a	chr19:38397049-38397060
36	SP1	chr19:38396870-38398870	A549	lung:	n/a	chr19:38397677-38397691
37	POLR2A	chr19:38397369-38398106	HepG2	liver:	n/a	n/a
38	REST	chr19:38396516-38398070	A549	lung:	n/a	n/a
39	FOSL2	chr19:38397550-38398028	HepG2	liver:	n/a	chr19:38397812-38397824
40	MAX	chr19:38396505-38397863	H1-hESC	embryonic stem cell:	n/a	chr19:38397081-38397090 chr19:38397082-38397089
41	TAF1	chr19:38397494-38398075	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr19:38397546-38398056	PFSK-1	brain:	n/a	n/a
43	HEY1	chr19:38397491-38398034	K562	blood:	n/a	n/a
44	POLR2A	chr19:38397457-38398266	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr19:38397333-38398210	U87	brain:	n/a	n/a
46	POLR2A	chr19:38397367-38397776	H1-hESC	embryonic stem cell:	n/a	n/a
47	BHLHE40	chr19:38397008-38398164	K562	blood:	n/a	chr19:38397785-38397801
48	TCF12	chr19:38396474-38399045	A549	lung:	n/a	chr19:38397051-38397058
49	BRCA1	chr19:38397532-38397975	Hela-S3	cervix:	n/a	n/a
50	YY1	chr19:38397146-38398225	HepG2	liver:	n/a	chr19:38398118-38398127 chr19:38398112-38398126 chr19:38398112-38398121 chr19:38398115-38398124 chr19:38397790-38397801 chr19:38398106-38398120 chr19:38398115-38398129

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38396344..38398889-chr19:38454374..38457525,4	MCF-7	breast:
3	chr19:38395370..38399266-chr19:38452571..38456602,5	MCF-7	breast:
4	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:

Variant related genes	Relation type
WDR87	TF binding region
SIPA1L3	TF binding region
ENSG00000105738	Chromatin interaction
ENSG00000268051	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs73623870	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73632107	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr19:38396400-38398600	Active TSS	Spleen	Spleen
2	chr19:38396400-38398800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:38396400-38400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:38396600-38398400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr19:38396600-38398400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:38396600-38398400	Active TSS	Fetal Brain Female	brain
7	chr19:38396600-38398400	Active TSS	Fetal Lung	lung
8	chr19:38396600-38398400	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr19:38396600-38398400	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr19:38396600-38398400	Active TSS	Rectal Smooth Muscle	rectum
11	chr19:38396600-38398400	Active TSS	K562	blood
12	chr19:38396600-38398600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:38396600-38398800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:38396600-38398800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:38396600-38399000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr19:38396600-38399200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr19:38396800-38397600	Flanking Active TSS	Fetal Brain Male	brain
18	chr19:38396800-38398000	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr19:38396800-38398200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr19:38396800-38398400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:38396800-38398400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:38396800-38398400	Active TSS	Primary T cells from cord blood	blood
23	chr19:38396800-38398400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:38396800-38398400	Active TSS	Brain Anterior Caudate	brain
25	chr19:38396800-38398400	Active TSS	Brain Hippocampus Middle	brain
26	chr19:38396800-38398400	Active TSS	Colonic Mucosa	Colon
27	chr19:38396800-38398400	Active TSS	Colon Smooth Muscle	Colon
28	chr19:38396800-38398400	Active TSS	NHEK	skin
29	chr19:38396800-38398600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:38396800-38398600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:38396800-38398600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:38396800-38398600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:38396800-38398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:38396800-38398800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:38396800-38398800	Active TSS	Muscle Satellite Cultured Cells	--
36	chr19:38396800-38399000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:38396800-38399000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:38396800-38399000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:38397000-38397600	Active TSS	Fetal Heart	heart
40	chr19:38397000-38397800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr19:38397000-38398000	Active TSS	Brain Germinal Matrix	brain
42	chr19:38397000-38398400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:38397000-38398400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:38397000-38398400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:38397000-38398400	Active TSS	Brain Angular Gyrus	brain
46	chr19:38397000-38398400	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr19:38397000-38398400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:38397000-38398400	Active TSS	Brain Substantia Nigra	brain
49	chr19:38397000-38398400	Active TSS	Duodenum Mucosa	Duodenum
50	chr19:38397000-38398400	Active TSS	Duodenum Smooth Muscle	Duodenum

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