Variant report

Variant	rs1870087
Chromosome Location	chr19:41256131-41256132
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	POLR2A	chr19:41255591-41257965	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:41255795-41257990	HepG2	liver:	n/a	n/a
5	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
6	USF1	chr19:41255954-41257350	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
7	CEBPB	chr19:41255999-41256871	K562	blood:	n/a	chr19:41256736-41256744
8	POLR2A	chr19:41255403-41257957	GM12891	blood:	n/a	n/a
9	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
10	TBP	chr19:41256104-41257861	K562	blood:	n/a	n/a
11	NFATC1	chr19:41255787-41256624	GM12878	blood:	n/a	n/a
12	ZBTB33	chr19:41256112-41257459	SK-N-SH	brain:	n/a	chr19:41257090-41257105 chr19:41257098-41257107
13	POLR2A	chr19:41255232-41256570	K562	blood:	n/a	n/a
14	HNF4G	chr19:41255951-41256587	HepG2	liver:	n/a	chr19:41256304-41256319
15	BCL3	chr19:41255259-41258065	A549	lung:	n/a	n/a
16	STAT1	chr19:41256004-41257721	GM12878	blood:	n/a	chr19:41257197-41257204
17	YY1	chr19:41255929-41256624	GM12878	blood:	n/a	chr19:41256386-41256398
18	YY1	chr19:41256052-41256597	GM12891	blood:	n/a	chr19:41256386-41256398
19	PBX3	chr19:41255724-41257395	A549	lung:	n/a	chr19:41257023-41257032
20	MXI1	chr19:41255751-41257913	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:41255546-41257864	HCT-116	colon:	n/a	n/a
22	USF1	chr19:41256021-41256819	H1-hESC	embryonic stem cell:	n/a	chr19:41256462-41256471 chr19:41256463-41256472 chr19:41256456-41256477 chr19:41256460-41256473 chr19:41256460-41256471 chr19:41256462-41256471 chr19:41256419-41256430
23	E2F4	chr19:41256044-41257453	MCF10A-Er-Src	breast:	n/a	chr19:41256643-41256654 chr19:41256760-41256770 chr19:41256736-41256745 chr19:41256721-41256736 chr19:41256805-41256815 chr19:41256721-41256736
24	POLR2A	chr19:41255259-41257957	HL-60	blood:	n/a	n/a
25	POLR2A	chr19:41255355-41257801	NB4	blood:	n/a	n/a
26	POLR2A	chr19:41255732-41257397	HCT-116	colon:	n/a	n/a
27	CEBPB	chr19:41255988-41256898	K562	blood:	n/a	chr19:41256736-41256744
28	TBP	chr19:41255849-41257768	Hela-S3	cervix:	n/a	n/a
29	TBL1XR1	chr19:41255729-41257824	K562	blood:	n/a	n/a
30	POLR2A	chr19:41255536-41257993	Hela-S3	cervix:	n/a	n/a
31	PML	chr19:41255985-41257923	K562	blood:	n/a	chr19:41256771-41256779
32	STAT5A	chr19:41255854-41256568	GM12878	blood:	n/a	n/a
33	YY1	chr19:41256054-41256529	GM12892	blood:	n/a	chr19:41256386-41256398
34	CHD1	chr19:41255798-41256518	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:41255295-41258005	U87	brain:	n/a	n/a
36	REST	chr19:41255871-41258036	H1-neurons	neurons:	n/a	n/a
37	SIX5	chr19:41256091-41257745	A549	lung:	n/a	n/a
38	POLR2A	chr19:41255276-41257951	GM12891	blood:	n/a	n/a
39	YY1	chr19:41256009-41256706	SK-N-SH	brain:	n/a	chr19:41256386-41256398
40	RCOR1	chr19:41255719-41256460	K562	blood:	n/a	n/a
41	ZBTB33	chr19:41255684-41257975	A549	lung:	n/a	chr19:41257090-41257105 chr19:41257098-41257107
42	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
43	MAFK	chr19:41256102-41256698	HepG2	liver:	n/a	n/a
44	UBTF	chr19:41255869-41256467	K562	blood:	n/a	n/a
45	ATF2	chr19:41255892-41256641	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:41256017-41257761	HEK293	kidney:	n/a	n/a
47	BHLHE40	chr19:41255391-41257820	K562	blood:	n/a	chr19:41256462-41256471 chr19:41256463-41256472 chr19:41256456-41256477 chr19:41256460-41256473 chr19:41256462-41256471
48	POLR2A	chr19:41255721-41258007	GM12878	blood:	n/a	n/a
49	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
50	NFIC	chr19:41256085-41256621	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
2	chr13:111365475..111366292-chr19:41255848..41256558,2	Hela-S3	cervix:
3	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
4	chr19:41082129..41084725-chr19:41255576..41257148,2	K562	blood:
5	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
6	chr19:41254747..41256268-chr19:41303480..41305851,2	MCF-7	breast:
7	chr19:41253175..41255589-chr19:41255801..41257660,2	MCF-7	breast:
8	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
9	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
10	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
11	chr19:41206945..41208497-chr19:41254996..41257251,2	K562	blood:
12	chr19:41246355..41251647-chr19:41252986..41257062,8	MCF-7	breast:
13	chr19:41194676..41198444-chr19:41254531..41258137,9	MCF-7	breast:
14	chr19:41222057..41222984-chr19:41256051..41256852,2	MCF-7	breast:
15	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
16	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
17	chr19:41255216..41257049-chr19:41286171..41288357,2	MCF-7	breast:
18	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
19	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
20	chr19:41254272..41257133-chr19:41310784..41312768,2	MCF-7	breast:
21	chr19:41253829..41256175-chr19:41256460..41259109,2	K562	blood:
22	chr19:41194241..41198233-chr19:41254859..41260401,9	K562	blood:
23	chr19:41254948..41257942-chr19:41767479..41769277,2	MCF-7	breast:
24	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
25	chr19:41191987..41193561-chr19:41255476..41257809,2	K562	blood:
26	chr19:41194241..41200533-chr19:41254244..41257966,10	K562	blood:
27	chr19:41081293..41083629-chr19:41254991..41257076,2	K562	blood:
28	chr19:41255938..41256570-chr5:10250352..10251225,2	Hela-S3	cervix:
29	chr19:41253320..41258890-chr19:41311950..41315573,6	MCF-7	breast:

Variant related genes	Relation type
SNRPA	TF binding region
C19orf54	TF binding region
ENSG00000261857	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000150753	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10407351	0.83[EUR][1000 genomes]
rs10425765	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11083566	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11548478	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12151251	0.87[ASN][1000 genomes]
rs12976551	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1469427	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1870086	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288451	0.85[CEU][hapmap]
rs2290692	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2290693	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2369302	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3745216	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs4802085	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4802086	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs4803363	0.96[ASN][1000 genomes]
rs7248468	1.00[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7248570	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7251246	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7255821	0.84[ASN][1000 genomes]
rs7257602	0.87[ASW][hapmap];0.92[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs7260405	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8111960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs890934	0.93[YRI][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1870087	LIN7B	cis	parietal	SCAN
rs1870087	ADCK4	cis	Nerve Tibial	GTEx
rs1870087	KCNN4	cis	cerebellum	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	chr19:41255200-41256200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:41255200-41256200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:41255200-41256200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:41255200-41256200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr19:41255200-41256200	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr19:41255200-41256200	Flanking Active TSS	A549	lung
8	chr19:41255200-41256200	Flanking Active TSS	Hela-S3	cervix
9	chr19:41255200-41256200	Flanking Active TSS	K562	blood
10	chr19:41255200-41256400	Flanking Active TSS	HMEC	breast
11	chr19:41255200-41256400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr19:41255400-41256200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:41255400-41256200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:41255400-41256200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:41255400-41256200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr19:41255400-41256200	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr19:41255400-41256200	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr19:41255400-41256200	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr19:41255400-41256200	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr19:41255400-41256200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr19:41255400-41256200	Flanking Active TSS	Fetal Brain Female	brain
22	chr19:41255400-41256200	Flanking Active TSS	Fetal Intestine Large	intestine
23	chr19:41255400-41256200	Flanking Active TSS	Stomach Mucosa	stomach
24	chr19:41255400-41256200	Flanking Active TSS	HSMMtube	muscle
25	chr19:41255400-41256200	Flanking Active TSS	NHEK	skin
26	chr19:41255400-41256400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr19:41255400-41256400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr19:41255400-41256400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:41255400-41256400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:41255400-41258200	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:41255400-41258200	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr19:41255400-41258600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr19:41255400-41258600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:41255600-41256200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr19:41255600-41256200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr19:41255600-41256200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:41255600-41256200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:41255600-41256200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr19:41255600-41256200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr19:41255600-41256200	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr19:41255600-41256200	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr19:41255600-41256200	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr19:41255600-41256200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr19:41255600-41256200	Flanking Active TSS	Colonic Mucosa	Colon
45	chr19:41255600-41256200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr19:41255600-41256200	Flanking Active TSS	Placenta	Placenta
47	chr19:41255600-41256200	Flanking Active TSS	Fetal Thymus	thymus
48	chr19:41255600-41256200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:41255600-41256200	Flanking Active TSS	Thymus	Thymus
50	chr19:41255600-41256200	Flanking Active TSS	NHDF-Ad	bronchial

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