Variant report

Variant	rs10404567
Chromosome Location	chr19:38397213-38397214
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	TAF1	chr19:38396940-38398238	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr19:38396994-38398157	GM19099	blood:	n/a	n/a
3	E2F6	chr19:38396670-38397732	H1-hESC	embryonic stem cell:	n/a	chr19:38397674-38397685 chr19:38397430-38397439
4	POLR2A	chr19:38396886-38398186	MCF-7	breast:	n/a	n/a
5	MXI1	chr19:38396701-38398350	HepG2	liver:	n/a	n/a
6	HMGN3	chr19:38397047-38398303	K562	blood:	n/a	n/a
7	PAX5	chr19:38397073-38398331	GM12892	blood:	n/a	chr19:38397430-38397439 chr19:38397894-38397904
8	POLR2A	chr19:38396978-38397401	HUVEC	blood vessel:	n/a	n/a
9	ZEB1	chr19:38396938-38397228	GM12878	blood:	n/a	chr19:38397049-38397060
10	MAZ	chr19:38396965-38398172	HepG2	liver:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
11	MAZ	chr19:38396945-38398347	IMR90	lung:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
12	MAX	chr19:38396948-38397349	K562	blood:	n/a	chr19:38397081-38397090 chr19:38397082-38397089
13	MAX	chr19:38396600-38398287	NB4	blood:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
14	GATA3	chr19:38396587-38397823	MCF-7	breast:	n/a	n/a
15	POLR2A	chr19:38397024-38397334	GM12891	blood:	n/a	n/a
16	MYC	chr19:38396948-38398019	K562	blood:	n/a	chr19:38397081-38397090 chr19:38397082-38397089
17	MXI1	chr19:38396961-38398476	H1-hESC	embryonic stem cell:	n/a	n/a
18	RELA	chr19:38397063-38398062	GM18951	blood:	n/a	n/a
19	TAF1	chr19:38396757-38398154	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZEB1	chr19:38396873-38397895	GM12878	blood:	n/a	chr19:38397049-38397060
21	SP1	chr19:38396870-38398870	A549	lung:	n/a	chr19:38397677-38397691
22	POLR2A	chr19:38396928-38397349	HepG2	liver:	n/a	n/a
23	REST	chr19:38396516-38398070	A549	lung:	n/a	n/a
24	MYC	chr19:38396922-38397333	MCF-7	breast:	n/a	chr19:38397081-38397090 chr19:38397082-38397089
25	MAX	chr19:38396505-38397863	H1-hESC	embryonic stem cell:	n/a	chr19:38397081-38397090 chr19:38397082-38397089
26	BHLHE40	chr19:38397008-38398164	K562	blood:	n/a	chr19:38397785-38397801
27	TCF12	chr19:38396474-38399045	A549	lung:	n/a	chr19:38397051-38397058
28	YY1	chr19:38397146-38398225	HepG2	liver:	n/a	chr19:38398118-38398127 chr19:38398112-38398126 chr19:38398112-38398121 chr19:38398115-38398124 chr19:38397790-38397801 chr19:38398106-38398120 chr19:38398115-38398129
29	POLR2A	chr19:38396898-38397290	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:38397062-38397317	HepG2	liver:	n/a	n/a
31	MAX	chr19:38396725-38397458	MCF-7	breast:	n/a	chr19:38397081-38397090 chr19:38397082-38397089
32	POLR2A	chr19:38397040-38397259	ProgFib	skin:	n/a	n/a
33	E2F6	chr19:38396891-38398164	K562	blood:	n/a	chr19:38397794-38397804 chr19:38397674-38397685 chr19:38398036-38398048 chr19:38398113-38398123 chr19:38398119-38398129 chr19:38397864-38397875 chr19:38397430-38397439
34	NRF1	chr19:38397072-38398229	SK-N-SH	brain:	n/a	chr19:38397799-38397808 chr19:38397345-38397356 chr19:38397426-38397440 chr19:38397429-38397440 chr19:38397311-38397322 chr19:38397322-38397333 chr19:38397429-38397443 chr19:38397431-38397440
35	NRF1	chr19:38397146-38397679	H1-hESC	embryonic stem cell:	n/a	chr19:38397345-38397356 chr19:38397426-38397440 chr19:38397429-38397440 chr19:38397311-38397322 chr19:38397322-38397333 chr19:38397429-38397443 chr19:38397431-38397440
36	CREB1	chr19:38396822-38398102	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:38396879-38398820	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr19:38396984-38398177	GM12892	blood:	n/a	n/a
39	KAP1	chr19:38396481-38398494	HEK293	kidney:	n/a	n/a
40	POLR2A	chr19:38396943-38398925	GM12891	blood:	n/a	n/a
41	POLR2A	chr19:38397028-38397324	HepG2	liver:	n/a	n/a
42	MAX	chr19:38396546-38398638	A549	lung:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
43	POLR2A	chr19:38397015-38397355	GM12892	blood:	n/a	n/a
44	POLR2A	chr19:38396895-38398292	MCF-7	breast:	n/a	n/a
45	POLR2A	chr19:38396965-38398191	HepG2	liver:	n/a	n/a
46	ELF1	chr19:38396960-38398305	GM12878	blood:	n/a	chr19:38398119-38398131 chr19:38398115-38398124 chr19:38397465-38397477 chr19:38397698-38397711
47	YY1	chr19:38397155-38397472	GM12878	blood:	n/a	n/a
48	ELF1	chr19:38397050-38398079	A549	lung:	n/a	chr19:38397465-38397477 chr19:38397698-38397711
49	BACH1	chr19:38397033-38397471	H1-hESC	embryonic stem cell:	n/a	n/a
50	SIN3AK20	chr19:38397094-38398005	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38396622..38397251-chr19:38480705..38481339,2	MCF-7	breast:
3	chr19:38396344..38398889-chr19:38454374..38457525,4	MCF-7	breast:
4	chr19:38395169..38397247-chr19:38624006..38625542,2	MCF-7	breast:
5	chr19:38395370..38399266-chr19:38452571..38456602,5	MCF-7	breast:
6	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:

Variant related genes	Relation type
SIPA1L3	TF binding region
ENSG00000268051	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10401637	0.86[EUR][1000 genomes]
rs10401968	0.81[EUR][1000 genomes]
rs10402530	0.82[EUR][1000 genomes]
rs10409402	0.80[EUR][1000 genomes]
rs10409487	0.80[EUR][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap]
rs10420891	0.82[EUR][1000 genomes]
rs10427125	0.82[EUR][1000 genomes]
rs1119229	0.88[CEU][hapmap]
rs11878269	0.81[EUR][1000 genomes]
rs11879180	0.82[EUR][1000 genomes]
rs1291	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs12974225	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs12975057	0.82[EUR][1000 genomes]
rs1643462	0.85[EUR][1000 genomes]
rs1643463	0.85[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs1643467	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs1643468	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1643469	0.87[EUR][1000 genomes]
rs1725477	0.85[EUR][1000 genomes]
rs1725478	0.85[EUR][1000 genomes]
rs1725480	0.85[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs1725483	0.85[EUR][1000 genomes]
rs1725485	0.85[EUR][1000 genomes]
rs1725487	0.85[EUR][1000 genomes]
rs1725488	0.83[EUR][1000 genomes]
rs1725494	0.86[EUR][1000 genomes]
rs1725499	0.88[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs241932	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2544718	0.86[EUR][1000 genomes]
rs2909093	0.83[ASW][hapmap];0.94[CEU][hapmap];0.92[TSI][hapmap]
rs2909098	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972437	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972438	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972439	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs3095726	0.93[CEU][hapmap]
rs35209753	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353398	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353399	0.89[EUR][1000 genomes]
rs353400	0.89[EUR][1000 genomes]
rs353402	0.89[EUR][1000 genomes]
rs353403	0.87[EUR][1000 genomes]
rs353404	0.89[EUR][1000 genomes]
rs353407	0.89[EUR][1000 genomes]
rs353410	0.88[CEU][hapmap]
rs353411	0.88[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353415	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs353416	0.89[EUR][1000 genomes]
rs353417	0.89[EUR][1000 genomes]
rs353419	0.89[EUR][1000 genomes]
rs353420	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353421	0.89[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353424	0.89[EUR][1000 genomes]
rs353425	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353426	0.87[EUR][1000 genomes]
rs353427	0.89[EUR][1000 genomes]
rs353428	0.85[EUR][1000 genomes]
rs353429	0.82[EUR][1000 genomes]
rs353430	0.86[EUR][1000 genomes]
rs3786869	0.87[CEU][hapmap]
rs3848626	0.81[EUR][1000 genomes]
rs4239516	0.87[CEU][hapmap]
rs4802135	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4803509	0.81[EUR][1000 genomes]
rs4803524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4803551	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs4803573	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs58449039	0.82[EUR][1000 genomes]
rs705491	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs705492	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs705493	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs705494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705495	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs705500	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7250409	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7250571	0.86[EUR][1000 genomes]
rs7250868	0.86[EUR][1000 genomes]
rs7252010	0.85[EUR][1000 genomes]
rs7257125	0.81[EUR][1000 genomes]
rs7258597	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752878	0.85[EUR][1000 genomes]
rs8101752	0.81[EUR][1000 genomes]
rs8101858	0.83[EUR][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs8104076	0.81[EUR][1000 genomes]
rs8107341	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8112706	1.00[CEU][hapmap]
rs8113521	0.88[CEU][hapmap]
rs8182498	0.82[EUR][1000 genomes]
rs833895	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs833896	0.84[EUR][1000 genomes]
rs833897	0.85[EUR][1000 genomes]
rs833898	0.85[EUR][1000 genomes]
rs833914	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs833926	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs856300	0.94[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs856304	1.00[CEU][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs9304572	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10404567	ZNF571	cis	multi-tissue	Pritchard
rs10404567	PHLDB3	cis	parietal	SCAN
rs10404567	DMPK	cis	parietal	SCAN
rs10404567	CBLC	cis	parietal	SCAN
rs10404567	AXL	cis	cerebellum	SCAN
rs10404567	PAFAH1B3	cis	cerebellum	SCAN
rs10404567	WDR87	cis	Thyroid	GTEx
rs10404567	PHLDB3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38396400-38397400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr19:38396400-38398600	Active TSS	Spleen	Spleen
3	chr19:38396400-38398800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:38396400-38400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:38396600-38397400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr19:38396600-38397400	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr19:38396600-38397400	Flanking Active TSS	Dnd41	blood
8	chr19:38396600-38398400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr19:38396600-38398400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:38396600-38398400	Active TSS	Fetal Brain Female	brain
11	chr19:38396600-38398400	Active TSS	Fetal Lung	lung
12	chr19:38396600-38398400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr19:38396600-38398400	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr19:38396600-38398400	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:38396600-38398400	Active TSS	K562	blood
16	chr19:38396600-38398600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:38396600-38398800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:38396600-38398800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:38396600-38399000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr19:38396600-38399200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr19:38396800-38397400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:38396800-38397400	Flanking Active TSS	HMEC	breast
23	chr19:38396800-38397400	Flanking Active TSS	Osteobl	bone
24	chr19:38396800-38397600	Flanking Active TSS	Fetal Brain Male	brain
25	chr19:38396800-38398000	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr19:38396800-38398200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr19:38396800-38398400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:38396800-38398400	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr19:38396800-38398400	Active TSS	Primary T cells from cord blood	blood
30	chr19:38396800-38398400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:38396800-38398400	Active TSS	Brain Anterior Caudate	brain
32	chr19:38396800-38398400	Active TSS	Brain Hippocampus Middle	brain
33	chr19:38396800-38398400	Active TSS	Colonic Mucosa	Colon
34	chr19:38396800-38398400	Active TSS	Colon Smooth Muscle	Colon
35	chr19:38396800-38398400	Active TSS	NHEK	skin
36	chr19:38396800-38398600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr19:38396800-38398600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:38396800-38398600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:38396800-38398600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:38396800-38398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:38396800-38398800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:38396800-38398800	Active TSS	Muscle Satellite Cultured Cells	--
43	chr19:38396800-38399000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:38396800-38399000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:38396800-38399000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:38397000-38397400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr19:38397000-38397400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr19:38397000-38397400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:38397000-38397400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr19:38397000-38397400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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