Variant report

Variant	rs2074175
Chromosome Location	chr19:18700047-18700048
allele	A/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	chr19:18698432-18704772	HepG2	liver:	n/a	n/a
2	ZC3H11A	chr19:18700021-18701633	K562	blood:	n/a	n/a
3	CEBPD	chr19:18699371-18700588	HepG2	liver:	n/a	n/a
4	MXI1	chr19:18699464-18700802	Hela-S3	cervix:	n/a	n/a
5	MAX	chr19:18698458-18701025	HepG2	liver:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
6	POLR2A	chr19:18699333-18700873	Hela-S3	cervix:	n/a	n/a
7	SIN3AK20	chr19:18699809-18700249	PFSK-1	brain:	n/a	n/a
8	EP300	chr19:18699339-18700171	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:18699287-18700931	K562	blood:	n/a	n/a
10	EGR1	chr19:18699727-18700220	ECC-1	luminal epithelium:	n/a	chr19:18699935-18699948 chr19:18699937-18699947 chr19:18699884-18699898 chr19:18699938-18699947 chr19:18699937-18699947 chr19:18699931-18699953 chr19:18699936-18699947 chr19:18699889-18699902 chr19:18699935-18699948 chr19:18699934-18699949 chr19:18699935-18699948 chr19:18699935-18699949 chr19:18699936-18699950 chr19:18699936-18699947
11	ELF1	chr19:18698919-18700973	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:18699241-18700733	HUVEC	blood vessel:	n/a	n/a
13	HA-E2F1	chr19:18699572-18700723	MCF-7	breast:	n/a	chr19:18699894-18699903 chr19:18699923-18699932
14	MAX	chr19:18698953-18700664	NB4	blood:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
15	CTCF	chr19:18699869-18700073	Spleen_OC	spleen:	n/a	chr19:18699925-18699938
16	FOXP2	chr19:18699749-18700146	SK-N-MC	brain:	n/a	n/a
17	TBL1XR1	chr19:18699301-18700392	K562	blood:	n/a	n/a
18	HDAC2	chr19:18699319-18700747	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:18699435-18700507	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:18699468-18700085	K562	blood:	n/a	n/a
21	FOXM1	chr19:18699069-18700111	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:18699398-18700524	MCF-7	breast:	n/a	n/a
23	POLR2A	chr19:18699344-18700583	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:18699434-18700548	Gliobla	brain:	n/a	n/a
25	POLR2A	chr19:18699190-18700536	GM12878	blood:	n/a	n/a
26	RFX5	chr19:18699450-18700084	Hela-S3	cervix:	n/a	n/a
27	MAX	chr19:18699250-18701052	MCF-7	breast:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
28	EGR1	chr19:18699538-18700206	MCF-7	breast:	n/a	chr19:18699935-18699948 chr19:18699937-18699947 chr19:18699884-18699898 chr19:18699938-18699947 chr19:18699937-18699947 chr19:18699931-18699953 chr19:18699936-18699947 chr19:18699889-18699902 chr19:18699935-18699948 chr19:18699934-18699949 chr19:18699935-18699948 chr19:18699935-18699949 chr19:18699936-18699950 chr19:18699936-18699947
29	TCF12	chr19:18699233-18700737	ECC-1	luminal epithelium:	n/a	n/a
30	TAF1	chr19:18699269-18700182	K562	blood:	n/a	n/a
31	POLR2A	chr19:18698422-18702101	K562	blood:	n/a	n/a
32	KAP1	chr19:18699051-18700904	HEK293	kidney:	n/a	n/a
33	POLR2A	chr19:18699444-18700925	MCF10A-Er-Src	breast:	n/a	n/a
34	TAF1	chr19:18699322-18700357	PFSK-1	brain:	n/a	n/a
35	MAX	chr19:18699732-18700846	MCF-7	breast:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
36	REST	chr19:18699385-18700048	HepG2	liver:	n/a	chr19:18699587-18699600
37	ZBTB7A	chr19:18699187-18700809	ECC-1	luminal epithelium:	n/a	chr19:18699893-18699902
38	POLR2A	chr19:18699298-18701733	H1-hESC	embryonic stem cell:	n/a	n/a
39	FOXA1	chr19:18699311-18700808	HepG2	liver:	n/a	n/a
40	NFATC1	chr19:18699164-18700187	GM12878	blood:	n/a	n/a
41	TAF1	chr19:18699346-18700594	HepG2	liver:	n/a	n/a
42	BCLAF1	chr19:18699207-18700633	GM12878	blood:	n/a	chr19:18699897-18699906
43	POLR2A	chr19:18699269-18701040	HCT-116	colon:	n/a	n/a
44	PAX5	chr19:18699273-18700218	GM12878	blood:	n/a	n/a
45	JUND	chr19:18699306-18700561	K562	blood:	n/a	n/a
46	POLR2A	chr19:18699208-18700179	HUVEC	blood vessel:	n/a	n/a
47	BHLHE40	chr19:18699378-18700685	K562	blood:	n/a	n/a
48	MAX	chr19:18699272-18700647	K562	blood:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
49	ELK1	chr19:18699195-18700255	GM12878	blood:	n/a	n/a
50	EGR1	chr19:18699428-18700115	K562	blood:	n/a	chr19:18699935-18699948 chr19:18699937-18699947 chr19:18699884-18699898 chr19:18699938-18699947 chr19:18699937-18699947 chr19:18699931-18699953 chr19:18699936-18699947 chr19:18699889-18699902 chr19:18699935-18699948 chr19:18699934-18699949 chr19:18699935-18699948 chr19:18699935-18699949 chr19:18699936-18699950 chr19:18699936-18699947

No.	Distal block	Cell Line	Cell type
1	chr19:18667424..18670168-chr19:18699281..18701481,3	MCF-7	breast:
2	chr19:18699463..18701468-chr19:19028694..19031158,3	K562	blood:
3	chr19:18698544..18700812-chr19:18957924..18960532,2	MCF-7	breast:
4	chr19:18698512..18700358-chr19:18745222..18750244,4	K562	blood:
5	chr19:18669154..18672917-chr19:18697910..18700793,4	K562	blood:
6	chr19:18699463..18701468-chr19:19028694..19031158,2	K562	blood:
7	chr19:18681312..18685117-chr19:18698049..18701447,5	MCF-7	breast:
8	chr19:18653459..18656385-chr19:18699225..18703130,9	K562	blood:
9	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
10	chr19:18667076..18669031-chr19:18699935..18702117,2	K562	blood:
11	chr19:18495663..18499199-chr19:18698556..18701601,3	K562	blood:
12	chr19:18631688..18633803-chr19:18698894..18701519,3	MCF-7	breast:
13	chr19:18631032..18633728-chr19:18697675..18701681,7	MCF-7	breast:
14	chr19:18630919..18637145-chr19:18698949..18704438,10	K562	blood:
15	chr19:18698708..18701515-chr19:18746316..18749182,4	MCF-7	breast:
16	chr19:18629422..18634718-chr19:18699285..18702887,8	K562	blood:
17	chr19:18527544..18530023-chr19:18699407..18700970,2	K562	blood:
18	chr19:18547378..18549702-chr19:18699788..18702900,3	K562	blood:

Variant related genes	Relation type
C19orf60	TF binding region
ENSG00000264175	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000268030	Chromatin interaction
ENSG00000105671	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000268983	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10407212	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409392	0.90[JPT][hapmap];0.85[TSI][hapmap]
rs10415257	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043192	0.90[JPT][hapmap]
rs1862645	0.90[JPT][hapmap]
rs2057649	0.90[JPT][hapmap]
rs2074174	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079015	0.90[JPT][hapmap]
rs2238650	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2314664	0.90[JPT][hapmap]
rs2314665	0.90[JPT][hapmap]
rs2314666	0.85[JPT][hapmap]
rs3170474	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3761032	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs4808823	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808839	0.90[JPT][hapmap]
rs6417264	0.93[ASN][1000 genomes]
rs709679	0.90[JPT][hapmap]
rs7250192	0.90[JPT][hapmap]
rs7250623	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7252198	0.93[ASN][1000 genomes]
rs7256319	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs886242	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs916791	0.90[JPT][hapmap]

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	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv911288	chr19:18700047-18739497	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2074175	CYP4F8	cis	cerebellum	SCAN
rs2074175	RAB8A	cis	parietal	SCAN
rs2074175	UBA52	cis	lymphoblastoid	seeQTL
rs2074175	C19orf50	cis	lymphoblastoid	seeQTL
rs2074175	NDUFA13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18698600-18700800	Flanking Active TSS	Colonic Mucosa	Colon
2	chr19:18698600-18701200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr19:18698600-18701200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr19:18698600-18701200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:18698800-18700200	Enhancers	Fetal Heart	heart
6	chr19:18698800-18700400	Active TSS	Rectal Smooth Muscle	rectum
7	chr19:18698800-18701000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr19:18698800-18701400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:18698800-18701800	Active TSS	Fetal Brain Female	brain
10	chr19:18699000-18700400	Flanking Active TSS	Liver	Liver
11	chr19:18699000-18700800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:18699000-18701000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr19:18699000-18701000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr19:18699000-18701400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr19:18699000-18701600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:18699000-18701600	Active TSS	A549	lung
17	chr19:18699000-18701800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:18699000-18701800	Active TSS	Fetal Kidney	kidney
19	chr19:18699200-18700200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:18699200-18700400	Active TSS	Primary T cells from cord blood	blood
21	chr19:18699200-18700400	Active TSS	Aorta	Aorta
22	chr19:18699200-18700400	Active TSS	Brain Substantia Nigra	brain
23	chr19:18699200-18700400	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:18699200-18700400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:18699200-18700600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:18699200-18701000	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr19:18699200-18701000	Active TSS	Psoas Muscle	Psoas
28	chr19:18699200-18701200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr19:18699200-18701200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:18699200-18701400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:18699200-18701400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:18699200-18701400	Active TSS	HSMM	muscle
33	chr19:18699200-18701600	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr19:18699200-18701600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr19:18699200-18701800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr19:18699200-18701800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr19:18699200-18702000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:18699400-18700200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:18699400-18700200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:18699400-18700200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:18699400-18700200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr19:18699400-18700200	Active TSS	Brain Hippocampus Middle	brain
43	chr19:18699400-18700200	Active TSS	Fetal Intestine Small	intestine
44	chr19:18699400-18700200	Active TSS	Lung	lung
45	chr19:18699400-18700200	Active TSS	Spleen	Spleen
46	chr19:18699400-18700200	Active TSS	HSMMtube	muscle
47	chr19:18699400-18700200	Active TSS	NHLF	lung
48	chr19:18699400-18700200	Active TSS	Osteobl	bone
49	chr19:18699400-18700400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr19:18699400-18700400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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