Variant report

Variant	rs572660229
Chromosome Location	chr19:19174451-19174452
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	SP2	chr19:19174113-19174859	H1-hESC	embryonic stem cell:	n/a	chr19:19174675-19174698 chr19:19174532-19174555 chr19:19174397-19174420
2	GABPA	chr19:19174143-19175000	MCF-7	breast:	n/a	n/a
3	PML	chr19:19173241-19174472	K562	blood:	n/a	n/a
4	POLR2A	chr19:19174059-19175188	GM18951	blood:	n/a	n/a
5	POLR2A	chr19:19174076-19174919	HCT-116	colon:	n/a	n/a
6	POLR2A	chr19:19173887-19174997	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:19173957-19174834	H1-hESC	embryonic stem cell:	n/a	n/a
8	CUX1	chr19:19173902-19174464	K562	blood:	n/a	n/a
9	CHD2	chr19:19174019-19175094	H1-hESC	embryonic stem cell:	n/a	chr19:19174953-19174963
10	SP1	chr19:19174150-19174954	K562	blood:	n/a	chr19:19174510-19174519 chr19:19174519-19174540 chr19:19174510-19174520 chr19:19174748-19174769 chr19:19174509-19174521 chr19:19174757-19174767 chr19:19174358-19174369 chr19:19174803-19174812 chr19:19174511-19174520 chr19:19174510-19174519 chr19:19174801-19174813 chr19:19174509-19174521 chr19:19174510-19174520
11	ELF1	chr19:19174116-19175182	GM12878	blood:	n/a	n/a
12	RCOR1	chr19:19172800-19175463	IMR90	lung:	n/a	n/a
13	CHD2	chr19:19174014-19175056	Hela-S3	cervix:	n/a	chr19:19174953-19174963
14	TBL1XR1	chr19:19174409-19174849	K562	blood:	n/a	n/a
15	MXI1	chr19:19173889-19175237	GM12878	blood:	n/a	n/a
16	RFX5	chr19:19174118-19174825	GM12878	blood:	n/a	chr19:19174750-19174759
17	MYC	chr19:19173277-19175247	K562	blood:	n/a	n/a
18	CBX3	chr19:19173110-19174697	K562	blood:	n/a	n/a
19	MAX	chr19:19173910-19175008	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr19:19174162-19174904	Hela-S3	cervix:	n/a	n/a
21	JUND	chr19:19174222-19174745	HepG2	liver:	n/a	chr19:19174664-19174673
22	SP1	chr19:19174001-19175185	HepG2	liver:	n/a	chr19:19174510-19174519 chr19:19174519-19174540 chr19:19174510-19174520 chr19:19174969-19174978 chr19:19174748-19174769 chr19:19174509-19174521 chr19:19174757-19174767 chr19:19174358-19174369 chr19:19174803-19174812 chr19:19175167-19175177 chr19:19174511-19174520 chr19:19174510-19174519 chr19:19174801-19174813 chr19:19174509-19174521 chr19:19174510-19174520
23	IRF1	chr19:19174169-19175206	K562	blood:	n/a	chr19:19174801-19174815 chr19:19174756-19174770 chr19:19174749-19174758 chr19:19174507-19174521
24	POLR2A	chr19:19174257-19175099	MCF10A-Er-Src	breast:	n/a	n/a
25	ARID3A	chr19:19173214-19174819	K562	blood:	n/a	n/a
26	POLR2A	chr19:19174167-19174825	Hela-S3	cervix:	n/a	n/a
27	BCL3	chr19:19174009-19174838	A549	lung:	n/a	n/a
28	NFYA	chr19:19173698-19174878	GM12878	blood:	n/a	chr19:19174660-19174675 chr19:19174708-19174718 chr19:19174660-19174675 chr19:19174747-19174762 chr19:19174747-19174762 chr19:19174706-19174719 chr19:19174747-19174761
29	POLR2A	chr19:19173954-19175251	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:19173765-19175002	Hela-S3	cervix:	n/a	n/a
31	CHD2	chr19:19174130-19175115	GM12878	blood:	n/a	chr19:19174953-19174963
32	FOXM1	chr19:19174060-19175129	GM12878	blood:	n/a	n/a
33	EGR1	chr19:19174132-19174637	ECC-1	luminal epithelium:	n/a	chr19:19174378-19174385 chr19:19174375-19174389
34	EBF1	chr19:19174066-19174799	GM12878	blood:	n/a	chr19:19174280-19174290 chr19:19174364-19174375 chr19:19174364-19174373
35	POLR2A	chr19:19174032-19176008	GM12878	blood:	n/a	n/a
36	ETS1	chr19:19174414-19174715	A549	lung:	n/a	chr19:19174588-19174601
37	BRCA1	chr19:19174217-19174767	Hela-S3	cervix:	n/a	n/a
38	ATF2	chr19:19174248-19174743	H1-hESC	embryonic stem cell:	n/a	n/a
39	ELK1	chr19:19174311-19174839	Hela-S3	cervix:	n/a	n/a
40	HDAC2	chr19:19174121-19175216	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:19173827-19174887	SK-N-SH	brain:	n/a	n/a
42	MYBL2	chr19:19173674-19174920	HepG2	liver:	n/a	n/a
43	JUN	chr19:19172291-19175360	K562	blood:	n/a	chr19:19173411-19173418 chr19:19173406-19173417 chr19:19173409-19173418 chr19:19173408-19173420 chr19:19174664-19174673
44	RCOR1	chr19:19172826-19175177	K562	blood:	n/a	n/a
45	FOS	chr19:19174199-19174920	GM12878	blood:	n/a	chr19:19174664-19174673
46	PML	chr19:19173718-19174581	K562	blood:	n/a	n/a
47	NFIC	chr19:19174037-19174553	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:19173942-19175441	GM12892	blood:	n/a	n/a
49	PML	chr19:19174128-19175051	MCF-7	breast:	n/a	n/a
50	SP1	chr19:19173978-19174992	A549	lung:	n/a	chr19:19174510-19174519 chr19:19174519-19174540 chr19:19174510-19174520 chr19:19174969-19174978 chr19:19174748-19174769 chr19:19174509-19174521 chr19:19174757-19174767 chr19:19174358-19174369 chr19:19174803-19174812 chr19:19174511-19174520 chr19:19174510-19174519 chr19:19174801-19174813 chr19:19174509-19174521 chr19:19174510-19174520

No.	Distal block	Cell Line	Cell type
1	chr19:19172859..19177096-chr19:19213191..19220004,7	K562	blood:
2	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:
3	chr19:19141992..19145925-chr19:19172787..19177854,10	K562	blood:
4	chr19:19129913..19132824-chr19:19171752..19174736,2	K562	blood:
5	chr19:18943405..18943938-chr19:19173944..19174627,2	MCF-7	breast:
6	chr19:19162360..19163114-chr19:19173888..19174551,2	MCF-7	breast:
7	chr19:19170341..19177029-chr19:19229928..19235464,11	K562	blood:
8	chr19:19170465..19178046-chr19:19213939..19220242,15	K562	blood:
9	chr19:19109933..19111022-chr19:19173938..19174740,6	MCF-7	breast:
10	chr19:19042101..19044216-chr19:19173856..19175729,2	K562	blood:
11	chr19:19172595..19175925-chr19:19247411..19251399,4	MCF-7	breast:
12	chr19:19110096..19111022-chr19:19173704..19174740,6	MCF-7	breast:
13	chr19:19169419..19177029-chr19:19229685..19233171,13	K562	blood:
14	chr19:19161417..19167211-chr19:19171135..19175299,5	MCF-7	breast:
15	chr19:19141992..19145825-chr19:19171077..19177701,15	K562	blood:
16	chr12:6716092..6716619-chr19:19173988..19174537,2	HCT-116	colon:
17	chr19:19169646..19176667-chr19:19241603..19249514,19	K562	blood:

Variant related genes	Relation type
SLC25A42	TF binding region
ENSG00000064607	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000111642	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000064545	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	nsv543927	chr19:19147376-19178024	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv17267	chr19:19174047-19177125	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 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	chr19:19173000-19174600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:19173800-19175000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:19173800-19175000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:19173800-19175000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:19173800-19175000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:19173800-19175000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr19:19173800-19175200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr19:19173800-19175200	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr19:19173800-19175400	Active TSS	Rectal Smooth Muscle	rectum
10	chr19:19173800-19175600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:19174000-19174800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:19174000-19175000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr19:19174000-19175000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:19174000-19175000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:19174000-19175200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr19:19174000-19175200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr19:19174000-19175200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:19174000-19175200	Active TSS	Psoas Muscle	Psoas
19	chr19:19174000-19175400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:19174000-19175400	Active TSS	Aorta	Aorta
21	chr19:19174000-19176200	Active TSS	Gastric	stomach
22	chr19:19174000-19176200	Active TSS	Ovary	ovary
23	chr19:19174000-19176400	Active TSS	Fetal Kidney	kidney
24	chr19:19174000-19176400	Active TSS	Right Atrium	heart
25	chr19:19174000-19176600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:19174000-19176600	Active TSS	Thymus	Thymus
27	chr19:19174200-19175000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:19174200-19175000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:19174200-19175000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:19174200-19175000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:19174200-19175000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr19:19174200-19175000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:19174200-19175000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:19174200-19175000	Active TSS	Colonic Mucosa	Colon
35	chr19:19174200-19175000	Weak transcription	Fetal Brain Male	brain
36	chr19:19174200-19175000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr19:19174200-19175000	Active TSS	Right Ventricle	heart
38	chr19:19174200-19175000	Active TSS	Spleen	Spleen
39	chr19:19174200-19175200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:19174200-19175200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:19174200-19175200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:19174200-19175200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:19174200-19175200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:19174200-19175200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:19174200-19175200	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr19:19174200-19175200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:19174200-19175200	Active TSS	Brain Cingulate Gyrus	brain
48	chr19:19174200-19175200	Active TSS	Brain Germinal Matrix	brain
49	chr19:19174200-19175200	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr19:19174200-19175200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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