Variant report

Variant	rs2604874
Chromosome Location	chr19:41257816-41257817
allele	A/C
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	chr19:41255477-41257972	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:41255880-41257853	GM15510	blood:	n/a	n/a
3	TAF7	chr19:41256652-41257953	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:41255591-41257965	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:41255795-41257990	HepG2	liver:	n/a	n/a
6	MAX	chr19:41255999-41257948	H1-hESC	embryonic stem cell:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
7	MYC	chr19:41256146-41257842	K562	blood:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
8	POLR2A	chr19:41255403-41257957	GM12891	blood:	n/a	n/a
9	STAT5A	chr19:41256597-41257889	GM12878	blood:	n/a	chr19:41257197-41257204
10	MAX	chr19:41255844-41257827	Hela-S3	cervix:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
11	TBP	chr19:41256104-41257861	K562	blood:	n/a	n/a
12	USF1	chr19:41257355-41257892	A549	lung:	n/a	n/a
13	TAF1	chr19:41257458-41257829	HepG2	liver:	n/a	n/a
14	SIN3AK20	chr19:41257447-41257825	HepG2	liver:	n/a	n/a
15	YY1	chr19:41257537-41257984	GM12878	blood:	n/a	chr19:41257824-41257834
16	BCL3	chr19:41255259-41258065	A549	lung:	n/a	n/a
17	MXI1	chr19:41255751-41257913	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:41255546-41257864	HCT-116	colon:	n/a	n/a
19	MAX	chr19:41256223-41257862	H1-hESC	embryonic stem cell:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
20	CHD2	chr19:41256174-41257860	K562	blood:	n/a	n/a
21	POLR2A	chr19:41255259-41257957	HL-60	blood:	n/a	n/a
22	TBL1XR1	chr19:41255729-41257824	K562	blood:	n/a	n/a
23	POLR2A	chr19:41255536-41257993	Hela-S3	cervix:	n/a	n/a
24	PML	chr19:41255985-41257923	K562	blood:	n/a	chr19:41256771-41256779
25	POLR2A	chr19:41255295-41258005	U87	brain:	n/a	n/a
26	REST	chr19:41255871-41258036	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr19:41255276-41257951	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:41256564-41257957	K562	blood:	n/a	n/a
29	ZBTB33	chr19:41255684-41257975	A549	lung:	n/a	chr19:41257090-41257105 chr19:41257098-41257107
30	MAX	chr19:41255934-41257852	A549	lung:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
31	E2F6	chr19:41256154-41257854	A549	lung:	n/a	chr19:41256760-41256770 chr19:41256736-41256745 chr19:41256721-41256736 chr19:41256805-41256815 chr19:41256721-41256736 chr19:41256442-41256453
32	BHLHE40	chr19:41255391-41257820	K562	blood:	n/a	chr19:41256462-41256471 chr19:41256463-41256472 chr19:41256456-41256477 chr19:41256460-41256473 chr19:41256462-41256471
33	CTCF	chr19:41257680-41257830	GM06990	blood:	n/a	n/a
34	POLR2A	chr19:41255721-41258007	GM12878	blood:	n/a	n/a
35	MYC	chr19:41255359-41257881	K562	blood:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
36	TCF7L2	chr19:41255862-41257934	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr19:41255731-41257877	GM12878	blood:	n/a	n/a
38	RELA	chr19:41255787-41257831	GM18951	blood:	n/a	n/a
39	USF1	chr19:41255994-41257902	A549	lung:	n/a	chr19:41256462-41256471 chr19:41256463-41256472 chr19:41256456-41256477 chr19:41256460-41256473 chr19:41256460-41256471 chr19:41256462-41256471 chr19:41256419-41256430
40	TAF1	chr19:41256726-41257847	GM12891	blood:	n/a	n/a
41	POLR2A	chr19:41255251-41257877	K562	blood:	n/a	n/a
42	POLR2A	chr19:41256091-41257816	A549	lung:	n/a	n/a
43	TAF1	chr19:41255732-41257980	A549	lung:	n/a	n/a
44	YY1	chr19:41257533-41257912	K562	blood:	n/a	chr19:41257824-41257834
45	POLR2A	chr19:41256640-41257893	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:41255185-41257990	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:41255227-41257860	K562	blood:	n/a	n/a
48	RAD21	chr19:41257485-41257835	SK-N-SH_RA	brain:	n/a	n/a
49	RAD21	chr19:41257092-41257899	Hela-S3	cervix:	n/a	n/a
50	ARID3A	chr19:41256050-41257940	HepG2	liver:	n/a	chr19:41256721-41256736

No.	Distal block	Cell Line	Cell type
1	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
2	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
3	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
4	chr11:65190254..65190996-chr19:41257060..41258041,2	Hela-S3	cervix:
5	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
6	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
7	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
8	chr19:41253829..41256175-chr19:41256460..41259109,2	K562	blood:
9	chr19:41194676..41198444-chr19:41254531..41258137,9	MCF-7	breast:
10	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
11	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
12	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
13	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
14	chr19:41194241..41198233-chr19:41254859..41260401,9	K562	blood:
15	chr19:41254948..41257942-chr19:41767479..41769277,2	MCF-7	breast:
16	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
17	chr19:41194241..41200533-chr19:41254244..41257966,10	K562	blood:
18	chr19:41253320..41258890-chr19:41311950..41315573,6	MCF-7	breast:

Variant related genes	Relation type
C19orf54	TF binding region
ENSG00000245532	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000171570	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1457141	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2254343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2369302	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs2607420	0.96[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7254893	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1793665	chr19:41249508-41258355	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
4	esv1803061	chr19:41249508-41258355	Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
5	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
6	esv1798663	chr19:41256519-41258355	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
7	esv1799699	chr19:41256519-41258355	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
8	esv1795486	chr19:41256581-41257816	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	35 gene(s)	inside rSNPs	diseases
9	esv1797942	chr19:41256581-41257816	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	35 gene(s)	inside rSNPs	diseases
10	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2604874	KCNN4	cis	cerebellum	SCAN
rs2604874	DHDH	cis	parietal	SCAN
rs2604874	C19orf54	Cis_1M	lymphoblastoid	RTeQTL
rs2604874	PPFIA3	cis	parietal	SCAN
rs2604874	C19orf54	cis	Lymphoblastoid	GTEx
rs2604874	SULT2B1	cis	cerebellum	SCAN
rs2604874	C19orf54	cis	lymphoblastoid	seeQTL
rs2604874	C19orf54	cis	Thyroid	GTEx
rs2604874	LIN7B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41254600-41259200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:41255400-41258200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:41255400-41258200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:41255400-41258600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:41255400-41258600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:41255600-41258000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr19:41255600-41258200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:41255600-41258600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:41255600-41258800	Active TSS	Gastric	stomach
10	chr19:41255600-41259000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr19:41255800-41258400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr19:41255800-41258400	Active TSS	Fetal Kidney	kidney
13	chr19:41255800-41258600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:41255800-41258600	Active TSS	Esophagus	oesophagus
15	chr19:41255800-41258600	Active TSS	GM12878-XiMat	blood
16	chr19:41255800-41258800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:41255800-41258800	Active TSS	Right Ventricle	heart
18	chr19:41255800-41259000	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr19:41256000-41258000	Active TSS	Aorta	Aorta
20	chr19:41256000-41258000	Active TSS	Left Ventricle	heart
21	chr19:41256000-41258000	Active TSS	Spleen	Spleen
22	chr19:41256000-41258200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:41256000-41258200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:41256000-41258200	Active TSS	Liver	Liver
25	chr19:41256000-41258200	Active TSS	Lung	lung
26	chr19:41256000-41258200	Active TSS	Psoas Muscle	Psoas
27	chr19:41256000-41258400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:41256000-41258400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:41256000-41258400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:41256000-41258600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:41256000-41258600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:41256000-41258600	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr19:41256000-41258600	Active TSS	Ovary	ovary
34	chr19:41256000-41258600	Active TSS	Pancreas	Pancrea
35	chr19:41256000-41258600	Active TSS	HSMM	muscle
36	chr19:41256000-41258800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:41256000-41258800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr19:41256200-41258000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:41256200-41258000	Active TSS	Fetal Stomach	stomach
40	chr19:41256200-41258200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:41256200-41258200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:41256200-41258200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:41256200-41258200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:41256200-41258200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:41256200-41258200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:41256200-41258200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:41256200-41258200	Active TSS	Brain Angular Gyrus	brain
48	chr19:41256200-41258200	Active TSS	Brain Anterior Caudate	brain
49	chr19:41256200-41258200	Active TSS	Brain Hippocampus Middle	brain
50	chr19:41256200-41258200	Active TSS	Colonic Mucosa	Colon

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