Variant report

Variant	rs2291001
Chromosome Location	chr19:38085332-38085333
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	CTCF	chr19:38085220-38085370	GM12871	blood:	n/a	n/a
2	CHD2	chr19:38084935-38086215	GM12878	blood:	n/a	n/a
3	MYC	chr19:38085116-38086307	K562	blood:	n/a	n/a
4	POLR2A	chr19:38085097-38085683	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:38085017-38085872	PANC-1	pancreas:	n/a	n/a
6	SP1	chr19:38084986-38085943	A549	lung:	n/a	chr19:38085423-38085433 chr19:38085423-38085433
7	IRF4	chr19:38085236-38085685	GM12878	blood:	n/a	n/a
8	IRF4	chr19:38085224-38085650	GM12878	blood:	n/a	n/a
9	STAT3	chr19:38084995-38085876	MCF10A-Er-Src	breast:	n/a	chr19:38085558-38085569
10	POLR2A	chr19:38085259-38085860	GM12878	blood:	n/a	n/a
11	ZKSCAN1	chr19:38084992-38086515	Hela-S3	cervix:	n/a	n/a
12	MAX	chr19:38084948-38086359	MCF-7	breast:	n/a	n/a
13	WRNIP1	chr19:38085316-38086067	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:38084964-38086230	GM12891	blood:	n/a	n/a
15	MAX	chr19:38084922-38086300	K562	blood:	n/a	n/a
16	POLR2A	chr19:38085155-38085779	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:38085113-38086710	H1-neurons	neurons:	n/a	n/a
18	BHLHE40	chr19:38085064-38085851	K562	blood:	n/a	n/a
19	EGR1	chr19:38085218-38085856	MCF-7	breast:	n/a	chr19:38085710-38085734 chr19:38085630-38085641 chr19:38085426-38085435 chr19:38085624-38085646 chr19:38085630-38085640 chr19:38085424-38085439 chr19:38085628-38085642 chr19:38085628-38085643 chr19:38085629-38085642 chr19:38085626-38085640 chr19:38085629-38085642 chr19:38085629-38085642
20	TCF12	chr19:38085032-38086046	ECC-1	luminal epithelium:	n/a	chr19:38085160-38085167
21	ETS1	chr19:38084999-38086036	A549	lung:	n/a	chr19:38085722-38085735
22	RCOR1	chr19:38085029-38086020	GM12878	blood:	n/a	n/a
23	YY1	chr19:38085132-38085660	GM12891	blood:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
24	JUND	chr19:38084970-38086143	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr19:38085065-38085935	A549	lung:	n/a	n/a
26	ELK1	chr19:38085056-38086209	GM12878	blood:	n/a	n/a
27	ZNF143	chr19:38085176-38086186	GM12878	blood:	n/a	chr19:38085715-38085733 chr19:38085722-38085731 chr19:38085724-38085733
28	MAX	chr19:38085072-38086328	H1-hESC	embryonic stem cell:	n/a	n/a
29	CEBPB	chr19:38085307-38085882	MCF-7	breast:	n/a	n/a
30	YY1	chr19:38085104-38085888	ECC-1	luminal epithelium:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
31	SIN3AK20	chr19:38085320-38085837	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:38085151-38085851	MCF-7	breast:	n/a	n/a
33	YY1	chr19:38085097-38086257	GM12892	blood:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
34	MYC	chr19:38085163-38085799	MCF-7	breast:	n/a	n/a
35	E2F4	chr19:38085217-38085781	MCF10A-Er-Src	breast:	n/a	n/a
36	YY1	chr19:38085211-38085864	SK-N-SH_RA	brain:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
37	MYC	chr19:38085215-38086176	K562	blood:	n/a	n/a
38	ZNF143	chr19:38085231-38086178	H1-hESC	embryonic stem cell:	n/a	chr19:38085715-38085733 chr19:38085722-38085731 chr19:38085724-38085733
39	MYC	chr19:38085029-38086325	MCF10A-Er-Src	breast:	n/a	n/a
40	MAZ	chr19:38085152-38085864	Hela-S3	cervix:	n/a	n/a
41	MAX	chr19:38085127-38086255	GM12878	blood:	n/a	n/a
42	FOS	chr19:38085122-38086492	MCF10A-Er-Src	breast:	n/a	chr19:38086284-38086295
43	ZEB1	chr19:38084919-38086349	HepG2	liver:	n/a	chr19:38085637-38085644 chr19:38085635-38085644 chr19:38085241-38085248
44	EP300	chr19:38084985-38086224	GM12878	blood:	n/a	n/a
45	CEBPB	chr19:38085268-38086033	HepG2	liver:	n/a	n/a
46	EGR1	chr19:38085140-38085922	MCF-7	breast:	n/a	chr19:38085710-38085734 chr19:38085630-38085641 chr19:38085426-38085435 chr19:38085624-38085646 chr19:38085630-38085640 chr19:38085424-38085439 chr19:38085628-38085642 chr19:38085628-38085643 chr19:38085629-38085642 chr19:38085626-38085640 chr19:38085629-38085642 chr19:38085629-38085642
47	ATF2	chr19:38085331-38085861	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:38085071-38085777	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr19:38085097-38085889	GM12878	blood:	n/a	n/a
50	RCOR1	chr19:38085157-38086364	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38084603..38087452-chr19:38269351..38271925,3	MCF-7	breast:
2	chr19:38083812..38086216-chr19:38209948..38211806,2	MCF-7	breast:
3	chr19:38085182..38087082-chr19:38268049..38270346,2	K562	blood:
4	chr19:38083338..38085691-chr19:38270478..38272116,2	K562	blood:
5	chr19:38078147..38079812-chr19:38083382..38085459,2	MCF-7	breast:

Variant related genes	Relation type
ZNF540	TF binding region
ENSG00000267422	Chromatin interaction
ENSG00000189144	Chromatin interaction
ENSG00000198182	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10419281	0.82[ASW][hapmap]
rs10445548	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs1871196	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2385180	1.00[ASW][hapmap]
rs35153242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.99[EUR][1000 genomes]
rs57943942	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62108291	0.84[EUR][1000 genomes]
rs62108306	0.82[EUR][1000 genomes]
rs7245855	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs7254009	0.82[ASW][hapmap]
rs7259272	0.92[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs73031330	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109103	1.00[ASW][hapmap]
rs8111790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2291001	ZNF781	trans	cerebellum	SCAN
rs2291001	C19orf61	cis	cerebellum	SCAN
rs2291001	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2291001	PVR	cis	parietal	SCAN
rs2291001	AC012309.5	cis	Thyroid	GTEx
rs2291001	AC012309.5	cis	Heart Left Ventricle	GTEx
rs2291001	ZNF781	cis	Thyroid	GTEx
rs2291001	AC012309.5	cis	Muscle Skeletal	GTEx
rs2291001	PAK4	cis	cerebellum	SCAN
rs2291001	AC012309.5	cis	Artery Tibial	GTEx
rs2291001	CCDC97	cis	cerebellum	SCAN
rs2291001	CEACAM3	cis	parietal	SCAN
rs2291001	RASGRP4	cis	parietal	SCAN
rs2291001	PLEKHG2	cis	cerebellum	SCAN
rs2291001	AC012309.5	cis	Esophagus Muscularis	GTEx
rs2291001	AC012309.5	cis	lung	GTEx
rs2291001	POU2F2	cis	parietal	SCAN
rs2291001	DMPK	cis	parietal	SCAN
rs2291001	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs2291001	PHLDB3	cis	cerebellum	SCAN
rs2291001	AC012309.5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38083600-38085400	ZNF genes & repeats	A549	lung
2	chr19:38084400-38085400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr19:38084400-38086000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:38084400-38086200	Active TSS	NHEK	skin
5	chr19:38084400-38086400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:38084400-38086400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:38084600-38085400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr19:38084600-38085400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr19:38084600-38085400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:38084600-38085400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr19:38084600-38085400	Flanking Active TSS	Fetal Heart	heart
12	chr19:38084600-38085400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:38084600-38085800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:38084600-38086000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:38084600-38086000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:38084600-38086000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr19:38084600-38086000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr19:38084600-38086000	Active TSS	K562	blood
19	chr19:38084600-38086200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr19:38084600-38086200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr19:38084600-38086200	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr19:38084600-38086200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:38084600-38086400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr19:38084600-38086400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr19:38084600-38086400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr19:38084600-38086400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:38084600-38086400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:38084600-38086400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr19:38084600-38086400	Active TSS	Colon Smooth Muscle	Colon
30	chr19:38084600-38086400	Active TSS	Esophagus	oesophagus
31	chr19:38084600-38086400	Active TSS	Fetal Kidney	kidney
32	chr19:38084600-38086400	Active TSS	Fetal Stomach	stomach
33	chr19:38084600-38086600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:38084600-38086600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr19:38084600-38086600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:38084600-38086600	Active TSS	Colonic Mucosa	Colon
37	chr19:38084600-38086600	Active TSS	Fetal Intestine Small	intestine
38	chr19:38084600-38086600	Active TSS	HSMM	muscle
39	chr19:38084600-38086600	Active TSS	NHLF	lung
40	chr19:38084600-38086800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:38084600-38086800	Active TSS	Fetal Intestine Large	intestine
42	chr19:38084600-38086800	Active TSS	HMEC	breast
43	chr19:38084600-38087000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:38084800-38085400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr19:38084800-38085400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:38084800-38085400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:38084800-38085400	Flanking Active TSS	Fetal Brain Male	brain
48	chr19:38084800-38086000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:38084800-38086000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:38084800-38086000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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