Variant report

Variant	rs1564203
Chromosome Location	chr19:39210961-39210962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39210940-39211090	HRPEpiC	eye:	n/a	chr19:39211029-39211037
2	TCF12	chr19:39210398-39211511	ECC-1	luminal epithelium:	n/a	chr19:39211104-39211114
3	REST	chr19:39210708-39211441	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39209151-39211490	K562	blood:	n/a	n/a
5	POLR2A	chr19:39209094-39212892	U87	brain:	n/a	n/a
6	POLR2A	chr19:39208578-39211524	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:39210420-39211075	A549	lung:	n/a	n/a
8	MAX	chr19:39209756-39210969	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr19:39208997-39211919	K562	blood:	n/a	n/a
10	POLR2A	chr19:39209073-39214530	K562	blood:	n/a	n/a
11	POLR2A	chr19:39210773-39211130	HepG2	liver:	n/a	n/a
12	NFIC	chr19:39209743-39211373	ECC-1	luminal epithelium:	n/a	chr19:39210932-39210949
13	POLR2A	chr19:39209212-39215383	A549	lung:	n/a	n/a
14	CTCF	chr19:39210900-39211050	HRPEpiC	eye:	n/a	chr19:39211029-39211037
15	POLR2A	chr19:39210641-39211145	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:39210901-39211461	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:39210446-39211025	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:39210867-39211595	K562	blood:	n/a	n/a
19	POLR2A	chr19:39210588-39210989	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:39210707-39211134	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr19:39210920-39211070	HA-sp	spinal cord:	n/a	chr19:39211029-39211037
22	POLR2A	chr19:39209202-39214711	K562	blood:	n/a	n/a
23	SIN3AK20	chr19:39209168-39211446	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr19:39210639-39211345	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr19:39210955-39211050	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZBTB7A	chr19:39209161-39211258	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr19:39206681-39226302	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr19:39210766-39211059	HUVEC	blood vessel:	n/a	n/a
29	NFIC	chr19:39210597-39211426	ECC-1	luminal epithelium:	n/a	chr19:39210932-39210949
30	POLR2A	chr19:39209161-39211240	HL-60	blood:	n/a	n/a
31	CTCF	chr19:39210960-39211110	HCPEpiC	choroid plexus:	n/a	chr19:39211029-39211037
32	ZBTB7A	chr19:39210166-39211208	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr19:39210467-39212805	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr19:39210379-39211569	A549	lung:	n/a	n/a
35	POLR2A	chr19:39210835-39211080	HCT-116	colon:	n/a	n/a
36	FOSL2	chr19:39210772-39211709	HepG2	liver:	n/a	chr19:39211544-39211553
37	POLR2A	chr19:39209088-39212955	U87	brain:	n/a	n/a
38	POLR2A	chr19:39209732-39211522	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr19:39210809-39211178	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr19:39206712-39220782	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr19:39210812-39211488	PFSK-1	brain:	n/a	n/a
42	BCL3	chr19:39210019-39211336	A549	lung:	n/a	n/a
43	EP300	chr19:39209651-39211562	ECC-1	luminal epithelium:	n/a	chr19:39210830-39210846

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39209590..39213111-chr19:39330256..39333147,3	MCF-7	breast:
2	chr19:39138734..39141158-chr19:39210569..39212913,2	MCF-7	breast:
3	chr19:39126170..39130709-chr19:39210922..39213805,4	MCF-7	breast:
4	chr19:39141347..39144030-chr19:39208371..39211834,3	MCF-7	breast:
5	chr19:39210151..39212274-chr19:39220710..39223551,2	MCF-7	breast:
6	chr19:39210554..39212101-chr19:39326682..39329322,2	MCF-7	breast:
7	chr19:39210217..39211879-chr19:39211993..39213574,2	MCF-7	breast:
8	chr19:39207862..39211804-chr19:39330654..39334530,3	MCF-7	breast:
9	chr19:39196541..39198571-chr19:39208360..39211296,2	K562	blood:
10	chr19:39151274..39153019-chr19:39209216..39212183,2	MCF-7	breast:
11	chr19:39209335..39212067-chr19:39340006..39342990,3	MCF-7	breast:
12	chr19:39138189..39142372-chr19:39210085..39214804,5	MCF-7	breast:

No data

Variant related genes	Relation type
ACTN4	TF binding region
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1031849	0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421863	0.80[CHB][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes]
rs10424568	0.95[CHD][hapmap];0.94[JPT][hapmap]
rs1060186	0.83[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083476	0.86[AMR][1000 genomes]
rs11665964	0.81[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11672576	0.89[AMR][1000 genomes]
rs12462503	0.88[ASW][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs12984247	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1985636	0.83[ASN][1000 genomes]
rs2080988	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2112649	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2112651	0.81[ASN][1000 genomes]
rs3786841	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3786843	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4347742	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4619518	0.89[AMR][1000 genomes]
rs4801861	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802743	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508813	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249585	0.89[AMR][1000 genomes]
rs7252630	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs749701	0.81[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs752067	0.94[ASW][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.81[ASN][1000 genomes]
rs755690	0.85[ASN][1000 genomes]
rs8099948	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8107877	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes]
rs888996	0.81[ASN][1000 genomes]
rs888997	0.88[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs9304576	0.83[ASW][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs9304577	0.88[JPT][hapmap]
rs936524	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1564203	RPS16	cis	parietal	SCAN
rs1564203	LGALS17A	cis	cerebellum	SCAN
rs1564203	CAPN12	cis	Heart Left Ventricle	GTEx
rs1564203	CAPN12	cis	Adipose Subcutaneous	GTEx
rs1564203	CAPN12	cis	lymphoblastoid	seeQTL
rs1564203	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs1564203	SFRS16	cis	parietal	SCAN
rs1564203	PPP1R13L	cis	cerebellum	SCAN
rs1564203	C19orf54	cis	parietal	SCAN
rs1564203	MEGF8	cis	cerebellum	SCAN
rs1564203	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs1564203	CAPN12	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39186400-39213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:39189400-39223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:39189800-39222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39190000-39218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:39190200-39222600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr19:39190200-39222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:39190400-39212000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:39190400-39212200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:39190400-39217000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:39190400-39218000	Strong transcription	Primary T cells from cord blood	blood
13	chr19:39190400-39222400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:39190400-39222600	Strong transcription	Dnd41	blood
15	chr19:39190600-39216400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr19:39190600-39217000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:39190600-39219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:39190600-39222800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:39190800-39220400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:39190800-39222600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr19:39190800-39222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:39190800-39222800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr19:39190800-39223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:39190800-39223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:39191000-39222400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:39191000-39222600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr19:39191400-39218800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:39192400-39221200	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:39199000-39215600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:39199000-39220400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr19:39199400-39215400	Weak transcription	Fetal Kidney	kidney
32	chr19:39199800-39214600	Strong transcription	HUVEC	blood vessel
33	chr19:39200400-39217200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr19:39202800-39221400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:39203400-39218600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:39204200-39223400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr19:39204600-39211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:39205000-39221000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:39205400-39211600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:39205600-39212200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr19:39205800-39211600	Weak transcription	Hela-S3	cervix
42	chr19:39205800-39212600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:39206800-39214200	Genic enhancers	Left Ventricle	heart
44	chr19:39206800-39220000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr19:39206800-39220000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:39207000-39212200	Strong transcription	Aorta	Aorta
47	chr19:39207000-39213600	Genic enhancers	Pancreas	Pancrea
48	chr19:39207000-39214800	Genic enhancers	Right Ventricle	heart
49	chr19:39207000-39219400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr19:39207000-39220200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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