Variant report

Variant	rs2617789
Chromosome Location	chr19:37960815-37960816
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	MXI1	chr19:37959788-37961066	GM12878	blood:	n/a	n/a
2	REST	chr19:37959526-37961104	H1-neurons	neurons:	n/a	n/a
3	EBF1	chr19:37960424-37960919	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:37959737-37960877	H1-neurons	neurons:	n/a	n/a
5	WRNIP1	chr19:37960033-37960851	GM12878	blood:	n/a	n/a
6	E2F6	chr19:37959712-37960912	A549	lung:	n/a	chr19:37959743-37959752
7	EBF1	chr19:37960578-37960869	GM12878	blood:	n/a	n/a
8	HA-E2F1	chr19:37959711-37960822	MCF-7	breast:	n/a	chr19:37959743-37959752
9	TCF7L2	chr19:37959802-37960859	PANC-1	pancreas:	n/a	n/a
10	GABPA	chr19:37959723-37960935	MCF-7	breast:	n/a	chr19:37959744-37959753 chr19:37959742-37959756 chr19:37959739-37959753 chr19:37959742-37959753
11	MXI1	chr19:37959532-37961158	SK-N-SH	brain:	n/a	n/a
12	ZNF263	chr19:37959731-37961090	HEK293-T-REx	kidney:	n/a	n/a
13	MAX	chr19:37959714-37960923	A549	lung:	n/a	n/a
14	GABPA	chr19:37959831-37960906	A549	lung:	n/a	n/a
15	EBF1	chr19:37960068-37960855	GM12878	blood:	n/a	n/a
16	MAX	chr19:37959893-37960829	SK-N-SH	brain:	n/a	n/a
17	SIN3AK20	chr19:37959743-37960897	PANC-1	pancreas:	n/a	n/a
18	TCF12	chr19:37959628-37960818	A549	lung:	n/a	n/a
19	NRF1	chr19:37959611-37961003	SK-N-SH	brain:	n/a	chr19:37959744-37959753 chr19:37959742-37959756 chr19:37959739-37959753 chr19:37959742-37959753
20	MAX	chr19:37959658-37961037	A549	lung:	n/a	n/a
21	POLR2A	chr19:37959701-37960907	H1-neurons	neurons:	n/a	n/a
22	SIX5	chr19:37959704-37960976	A549	lung:	n/a	chr19:37960182-37960191 chr19:37960760-37960769

No.	Distal block	Cell Line	Cell type
1	chr19:37960304..37962188-chr19:38144303..38146867,2	MCF-7	breast:
2	chr19:37958940..37961916-chr19:38146231..38147953,2	K562	blood:
3	chr19:37957751..37961901-chr19:37996099..37999727,6	MCF-7	breast:
4	chr19:37861996..37864602-chr19:37959702..37962085,2	MCF-7	breast:

Variant related genes	Relation type
ZNF569	TF binding region
ENSG00000266916	Chromatin interaction
ENSG00000120784	Chromatin interaction
ENSG00000189164	Chromatin interaction
ENSG00000188227	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1038085	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10403307	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10425671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11883392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1236810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1465434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530500	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap]
rs1871197	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2045909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2199644	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs256737	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256742	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256743	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972456	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs45483504	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62110388	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110389	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110390	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110392	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62110395	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110430	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs6508738	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7251097	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs7254170	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs73027379	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73027386	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108650	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109709	0.95[EUR][1000 genomes]

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	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2617789	CATSPERG	cis	parietal	SCAN
rs2617789	ITPKC	cis	cerebellum	SCAN
rs2617789	IGFL4	cis	parietal	SCAN
rs2617789	EXOSC5	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37956800-37961200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr19:37956800-37961200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:37956800-37961400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:37956800-37961400	Active TSS	NHLF	lung
5	chr19:37956800-37961600	Active TSS	Rectal Smooth Muscle	rectum
6	chr19:37957000-37961000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:37957000-37961000	Active TSS	Fetal Intestine Large	intestine
8	chr19:37957000-37961000	Active TSS	Right Ventricle	heart
9	chr19:37957000-37961200	Active TSS	Right Atrium	heart
10	chr19:37957000-37961400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr19:37957000-37961400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:37957000-37961400	Active TSS	NH-A	brain
13	chr19:37957000-37961400	Active TSS	NHDF-Ad	bronchial
14	chr19:37957200-37961000	Active TSS	HSMM	muscle
15	chr19:37957200-37961200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr19:37957200-37961200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:37957200-37961200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:37957200-37961400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:37957200-37961400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr19:37957400-37961000	Active TSS	Fetal Stomach	stomach
21	chr19:37957400-37961200	Active TSS	Psoas Muscle	Psoas
22	chr19:37957600-37961000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:37958200-37961000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:37958800-37961200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:37959000-37961000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:37959200-37961000	Active TSS	Colonic Mucosa	Colon
27	chr19:37959200-37961200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:37959400-37961000	Active TSS	Aorta	Aorta
29	chr19:37959400-37961000	Active TSS	Fetal Intestine Small	intestine
30	chr19:37959400-37961400	Active TSS	Muscle Satellite Cultured Cells	--
31	chr19:37959600-37961000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr19:37959600-37961000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:37959600-37961000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:37959600-37961000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr19:37959600-37961000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr19:37959600-37961000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:37959600-37961000	Active TSS	Esophagus	oesophagus
38	chr19:37959600-37961000	Active TSS	Left Ventricle	heart
39	chr19:37959600-37961000	Active TSS	Ovary	ovary
40	chr19:37959600-37961000	Active TSS	Pancreas	Pancrea
41	chr19:37959600-37961000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr19:37959600-37961000	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr19:37959600-37961200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:37959600-37961200	Active TSS	HMEC	breast
45	chr19:37959600-37961400	Active TSS	H9 Cell Line	embryonic stem cell
46	chr19:37959600-37961400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:37959600-37961400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr19:37959600-37961400	Active TSS	A549	lung
49	chr19:37959800-37961000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr19:37959800-37961000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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