Variant report

Variant	rs735571
Chromosome Location	chr19:42463447-42463448
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	SIX5	chr19:42463315-42463959	K562	blood:	n/a	chr19:42463595-42463604 chr19:42463593-42463602 chr19:42463562-42463576 chr19:42463712-42463721
2	GABPA	chr19:42463434-42463656	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr19:42463313-42464057	A549	lung:	n/a	n/a
4	KAP1	chr19:42462918-42463976	U2OS	brain:	n/a	n/a
5	TCF12	chr19:42463235-42463954	ECC-1	luminal epithelium:	n/a	chr19:42463554-42463564
6	RCOR1	chr19:42463423-42463897	K562	blood:	n/a	n/a
7	POLR2A	chr19:42462780-42463870	GM12891	blood:	n/a	n/a
8	YY1	chr19:42463306-42463961	HepG2	liver:	n/a	chr19:42463633-42463643
9	BHLHE40	chr19:42463009-42463825	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:42462700-42463860	K562	blood:	n/a	n/a
11	TCF12	chr19:42463169-42464047	A549	lung:	n/a	chr19:42463554-42463564
12	JUND	chr19:42463398-42463948	H1-hESC	embryonic stem cell:	n/a	chr19:42463611-42463621 chr19:42463611-42463621 chr19:42463611-42463621
13	TAF1	chr19:42463215-42463819	SK-N-SH	brain:	n/a	n/a
14	YY1	chr19:42462747-42464167	SK-N-SH	brain:	n/a	chr19:42463633-42463643 chr19:42464100-42464111 chr19:42464065-42464084
15	POLR2A	chr19:42463337-42463788	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr19:42462612-42463657	MCF-7	breast:	n/a	n/a
17	POLR2A	chr19:42463191-42463658	GM12878	blood:	n/a	n/a
18	ZBTB7A	chr19:42463038-42463660	K562	blood:	n/a	chr19:42463335-42463343
19	TAF1	chr19:42462411-42463812	A549	lung:	n/a	n/a
20	NFYA	chr19:42463401-42463571	Hela-S3	cervix:	n/a	n/a
21	RUNX3	chr19:42463341-42464017	GM12878	blood:	n/a	n/a
22	BHLHE40	chr19:42463088-42463575	A549	lung:	n/a	n/a
23	RELA	chr19:42463408-42463972	GM19099	blood:	n/a	n/a
24	TCF3	chr19:42463280-42463966	GM12878	blood:	n/a	chr19:42463551-42463564
25	POLR2A	chr19:42462717-42463786	GM19193	blood:	n/a	n/a
26	ELF1	chr19:42463324-42463774	HepG2	liver:	n/a	n/a
27	EP300	chr19:42463048-42464112	A549	lung:	n/a	n/a
28	JUND	chr19:42463437-42463658	HepG2	liver:	n/a	chr19:42463611-42463621 chr19:42463611-42463621 chr19:42463611-42463621
29	POLR2A	chr19:42463233-42463673	A549	lung:	n/a	n/a
30	GABPA	chr19:42463327-42463956	A549	lung:	n/a	n/a
31	CREB1	chr19:42463236-42464017	H1-hESC	embryonic stem cell:	n/a	n/a
32	BHLHE40	chr19:42463201-42463852	GM12878	blood:	n/a	n/a
33	MAX	chr19:42463411-42463991	K562	blood:	n/a	n/a
34	POLR2A	chr19:42463298-42463655	HepG2	liver:	n/a	n/a
35	YY1	chr19:42463294-42463969	K562	blood:	n/a	chr19:42463633-42463643
36	POLR2A	chr19:42463320-42463815	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr19:42462667-42463881	SK-N-SH	brain:	n/a	n/a
38	ATF3	chr19:42463156-42464093	A549	lung:	n/a	chr19:42463687-42463696
39	FOXA2	chr19:42463242-42464103	A549	lung:	n/a	n/a
40	CTCF	chr19:42463425-42464012	H1-hESC	embryonic stem cell:	n/a	n/a
41	SP1	chr19:42463295-42463874	GM12878	blood:	n/a	chr19:42463315-42463329 chr19:42463325-42463339 chr19:42463318-42463332 chr19:42463311-42463325
42	TAF1	chr19:42463283-42463647	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:42463329-42463718	H1-hESC	embryonic stem cell:	n/a	n/a
44	RCOR1	chr19:42463401-42463975	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr19:42462461-42463868	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr19:42463257-42463768	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr19:42462549-42463646	GM12878	blood:	n/a	n/a
48	CTBP2	chr19:42463189-42463979	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:42462684-42463711	Gliobla	brain:	n/a	n/a
50	TAF1	chr19:42462594-42463808	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42362135..42368129-chr19:42461941..42464761,7	MCF-7	breast:
2	chr19:42430426..42435985-chr19:42461209..42463660,4	K562	blood:
3	chr19:42379146..42381960-chr19:42461841..42465419,3	MCF-7	breast:
4	chr19:42361051..42365836-chr19:42460461..42465209,10	K562	blood:
5	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:
6	chr19:42461278..42463492-chr20:55838965..55841655,2	MCF-7	breast:
7	chr19:42361938..42366462-chr19:42459916..42465209,13	K562	blood:
8	chr19:42387951..42392334-chr19:42459610..42463737,7	MCF-7	breast:
9	chr19:42460531..42463518-chr19:42578179..42580939,2	K562	blood:
10	chr19:42460466..42464604-chr19:42577075..42581382,5	MCF-7	breast:
11	chr19:42385735..42391033-chr19:42460351..42463651,6	K562	blood:
12	chr19:42462261..42465397-chr19:42579731..42582911,4	MCF-7	breast:
13	chr19:42462621..42465324-chr19:42490447..42493373,2	MCF-7	breast:
14	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:

Variant related genes	Relation type
RABAC1	TF binding region
ENSG00000105372	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000105369	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000105409	Chromatin interaction
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10409822	0.84[ASN][1000 genomes]
rs10411814	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10416501	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419731	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10420264	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10424013	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11083642	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11665965	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11667048	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668332	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669448	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11878287	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971376	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12972751	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12975677	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1864207	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1965727	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081999	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745223	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826707	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61007366	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7246830	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7247727	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253563	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109192	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919390	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304600	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9676662	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9749440	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats 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
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs735571	RABAC1	cis	multi-tissue	Pritchard
rs735571	CCDC114	cis	cerebellum	SCAN
rs735571	SLC1A5	cis	parietal	SCAN
rs735571	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs735571	RABAC1	cis	lymphoblastoid	seeQTL
rs735571	TMEM143	cis	parietal	SCAN
rs735571	IGFL1	cis	parietal	SCAN
rs735571	ENSG00000105404	cis	multi-tissue	Pritchard
rs735571	ZNF230	cis	parietal	SCAN
rs735571	PVR	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42461800-42464000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr19:42462000-42464000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr19:42462200-42463800	Active TSS	Aorta	Aorta
4	chr19:42462200-42464000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr19:42462200-42464000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:42462400-42463600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:42462400-42463800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:42462400-42463800	Active TSS	Placenta Amnion	Placenta Amnion
9	chr19:42462400-42464000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:42462400-42464000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:42462400-42464000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr19:42462400-42464000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr19:42462400-42464000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:42462400-42464000	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr19:42462400-42464000	Active TSS	Fetal Kidney	kidney
16	chr19:42462400-42464000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:42462400-42464000	Active TSS	Right Atrium	heart
18	chr19:42462400-42464200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:42462600-42463600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr19:42462600-42463800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:42462600-42463800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr19:42462600-42463800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:42462600-42463800	Active TSS	Colon Smooth Muscle	Colon
24	chr19:42462600-42463800	Active TSS	Fetal Intestine Large	intestine
25	chr19:42462600-42463800	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr19:42462600-42463800	Active TSS	Stomach Mucosa	stomach
27	chr19:42462600-42463800	Active TSS	Hela-S3	cervix
28	chr19:42462600-42463800	Active TSS	K562	blood
29	chr19:42462600-42464000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:42462600-42464000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:42462600-42464000	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr19:42462600-42464000	Active TSS	Ovary	ovary
33	chr19:42462600-42464000	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr19:42462600-42464000	Active TSS	Small Intestine	intestine
35	chr19:42462600-42464000	Active TSS	HSMM	muscle
36	chr19:42462600-42464000	Active TSS	HSMMtube	muscle
37	chr19:42462600-42464200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr19:42462600-42464200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr19:42462600-42464200	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr19:42462800-42463600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:42462800-42463600	Active TSS	Primary monocytes fromperipheralblood	blood
42	chr19:42462800-42463600	Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr19:42462800-42463600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:42462800-42463600	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr19:42462800-42463600	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr19:42462800-42463600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:42462800-42463600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:42462800-42463600	Active TSS	Fetal Stomach	stomach
49	chr19:42462800-42463600	Active TSS	Spleen	Spleen
50	chr19:42462800-42463600	Active TSS	HUVEC	blood vessel

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