Variant report

Variant	rs1978423
Chromosome Location	chr19:18450713-18450714
allele	C/T
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	chr19:18450698-18450875	K562	blood:	n/a	n/a
2	RAD21	chr19:18450484-18450770	SK-N-SH_RA	brain:	n/a	chr19:18450625-18450644
3	RAD21	chr19:18450481-18450818	Hela-S3	cervix:	n/a	chr19:18450625-18450644
4	ZNF143	chr19:18450576-18451474	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:18450515-18450797	IMR90	lung:	n/a	chr19:18450626-18450647
6	CTCF	chr19:18450600-18450750	GM12869	blood:	n/a	chr19:18450626-18450647
7	HCFC1	chr19:18450661-18450793	K562	blood:	n/a	n/a
8	CTCF	chr19:18450580-18450730	SAEC	small airway:	n/a	chr19:18450626-18450647
9	CTCF	chr19:18450606-18450755	MCF-7	breast:	n/a	chr19:18450626-18450647
10	MAX	chr19:18450481-18450907	K562	blood:	n/a	n/a
11	ZBTB7A	chr19:18450572-18450875	K562	blood:	n/a	n/a
12	ZNF143	chr19:18450576-18451436	K562	blood:	n/a	n/a
13	SIN3A	chr19:18450612-18450898	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr19:18450620-18450770	NHDF-neo	bronchial:	n/a	chr19:18450626-18450647
15	JUND	chr19:18450516-18450854	K562	blood:	n/a	n/a
16	YY1	chr19:18450584-18450874	K562	blood:	n/a	n/a
17	CTCF	chr19:18450585-18450732	Medullo	brain:	n/a	chr19:18450626-18450647
18	CTCF	chr19:18450580-18450730	GM12871	blood:	n/a	chr19:18450626-18450647
19	RCOR1	chr19:18450614-18451557	K562	blood:	n/a	n/a
20	CTCF	chr19:18450554-18450727	GM12878	blood:	n/a	chr19:18450626-18450647
21	CTCF	chr19:18450530-18450757	SK-N-SH_RA	brain:	n/a	chr19:18450626-18450647
22	CTCF	chr19:18450390-18450843	K562	blood:	n/a	chr19:18450626-18450647
23	CTCF	chr19:18450600-18450750	HAc	cerebellar:	n/a	chr19:18450626-18450647
24	RCOR1	chr19:18450565-18451640	IMR90	lung:	n/a	n/a
25	CTCF	chr19:18450526-18450760	K562	blood:	n/a	chr19:18450626-18450647
26	CBX3	chr19:18450439-18451669	K562	blood:	n/a	n/a
27	MXI1	chr19:18450386-18452552	SK-N-SH	brain:	n/a	chr19:18452040-18452049 chr19:18452217-18452226 chr19:18452217-18452226 chr19:18452219-18452228
28	HCFC1	chr19:18450455-18451663	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr19:18450600-18450750	GM12868	blood:	n/a	chr19:18450626-18450647
30	MAZ	chr19:18450568-18452433	K562	blood:	n/a	chr19:18452220-18452229 chr19:18452218-18452227 chr19:18452217-18452227 chr19:18452218-18452227 chr19:18451380-18451390 chr19:18451569-18451579 chr19:18451556-18451566 chr19:18452218-18452227
31	CTCF	chr19:18450580-18450730	HMF	breast:	n/a	chr19:18450626-18450647
32	EP300	chr19:18450582-18450810	K562	blood:	n/a	chr19:18450730-18450744
33	CTCF	chr19:18450580-18450730	HL-60	blood:	n/a	chr19:18450626-18450647
34	CTCF	chr19:18450680-18450830	HCM	heart:	n/a	n/a
35	CTCF	chr19:18450538-18450719	HUVEC	blood vessel:	n/a	chr19:18450626-18450647
36	CTCF	chr19:18450580-18450730	A549	lung:	n/a	chr19:18450626-18450647
37	RCOR1	chr19:18450514-18451588	K562	blood:	n/a	n/a
38	CTCF	chr19:18450640-18450790	HFF-Myc	foreskin:	n/a	n/a
39	CTCF	chr19:18450580-18450730	HPF	lung:	n/a	chr19:18450626-18450647
40	CTCF	chr19:18450554-18450734	Hela-S3	cervix:	n/a	chr19:18450626-18450647
41	ARID3A	chr19:18450568-18450719	K562	blood:	n/a	n/a
42	CTCF	chr19:18450580-18450730	HRE	kidney:	n/a	chr19:18450626-18450647
43	CTCF	chr19:18450563-18450732	GM10266	blood:	n/a	chr19:18450626-18450647
44	RAD21	chr19:18450541-18450777	SK-N-SH_RA	brain:	n/a	chr19:18450625-18450644
45	CTCF	chr19:18450580-18450730	Hela-S3	cervix:	n/a	chr19:18450626-18450647
46	SMC3	chr19:18450487-18450849	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr19:18450580-18450730	AG09319	gingival:	n/a	chr19:18450626-18450647
48	CTCF	chr19:18450580-18450730	GM12873	blood:	n/a	chr19:18450626-18450647
49	CTCF	chr19:18450580-18450730	HBMEC	blood vessel:	n/a	chr19:18450626-18450647
50	CTCF	chr19:18450558-18450738	Gliobla	brain:	n/a	chr19:18450626-18450647

No.	Distal block	Cell Line	Cell type
1	chr19:18263193..18264879-chr19:18450426..18452528,2	K562	blood:
2	chr19:18450514..18452261-chr19:18530273..18532416,2	K562	blood:
3	chr19:18450174..18452696-chr19:18496613..18498593,2	MCF-7	breast:
4	chr19:18448228..18453626-chr19:18495351..18501647,22	K562	blood:
5	chr19:18450121..18451677-chr19:18546960..18548489,2	MCF-7	breast:
6	chr19:18429634..18433959-chr19:18449815..18453704,5	K562	blood:
7	chr19:18448952..18453435-chr19:18523841..18530143,7	K562	blood:
8	chr19:18449115..18453939-chr19:18483257..18487784,7	K562	blood:
9	chr19:18432103..18434677-chr19:18449671..18452769,4	MCF-7	breast:
10	chr19:18442556..18446502-chr19:18450638..18453378,4	MCF-7	breast:
11	chr19:18449803..18452751-chr19:18530696..18534160,4	MCF-7	breast:
12	chr19:18388917..18393354-chr19:18447866..18453758,9	MCF-7	breast:
13	chr19:18441208..18448128-chr19:18448861..18453326,10	K562	blood:

Variant related genes	Relation type
PGPEP1	TF binding region
ENSG00000130511	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000105647	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000239821	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000130520	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10401774	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10403547	1.00[ASN][1000 genomes]
rs10415319	1.00[ASN][1000 genomes]
rs10415765	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10423237	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10424419	1.00[ASN][1000 genomes]
rs1059022	1.00[CHB][hapmap]
rs11881039	1.00[ASN][1000 genomes]
rs11882198	1.00[ASN][1000 genomes]
rs16995488	1.00[GIH][hapmap]
rs28503677	1.00[ASN][1000 genomes]
rs4641872	1.00[GIH][hapmap];0.86[TSI][hapmap]
rs55887446	1.00[ASN][1000 genomes]
rs56104914	1.00[ASN][1000 genomes]
rs56326450	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6413435	1.00[CHB][hapmap]
rs6512259	1.00[ASN][1000 genomes]
rs66732430	1.00[ASN][1000 genomes]
rs67348050	1.00[ASN][1000 genomes]
rs7251555	1.00[ASN][1000 genomes]
rs7253758	1.00[ASN][1000 genomes]
rs7254789	1.00[CHB][hapmap]
rs7255983	1.00[ASN][1000 genomes]
rs73009442	1.00[ASN][1000 genomes]
rs8101249	1.00[CHB][hapmap]
rs8102478	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8102906	1.00[ASN][1000 genomes]
rs8112644	1.00[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	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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 miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
5	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
6	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1978423	TPM4	cis	parietal	SCAN
rs1978423	PGPEP1	cis	cerebellum	SCAN
rs1978423	RGS20	trans	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18440400-18450800	Weak transcription	Right Ventricle	heart
2	chr19:18440600-18450800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:18444000-18450800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:18444200-18451000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:18445000-18450800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:18445000-18451000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:18446600-18451000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:18446800-18450800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:18447400-18450800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:18448000-18450800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr19:18448600-18450800	Enhancers	Fetal Intestine Large	intestine
12	chr19:18448600-18450800	Enhancers	Fetal Intestine Small	intestine
13	chr19:18448600-18451000	Enhancers	Liver	Liver
14	chr19:18449200-18450800	Weak transcription	Left Ventricle	heart
15	chr19:18449200-18450800	Enhancers	Pancreas	Pancrea
16	chr19:18449400-18450800	Weak transcription	Fetal Heart	heart
17	chr19:18449800-18450800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr19:18450400-18450800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:18450400-18450800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr19:18450400-18450800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:18450400-18450800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr19:18450600-18450800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:18450600-18450800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:18450600-18450800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr19:18450600-18450800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:18450600-18450800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr19:18450600-18450800	Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr19:18450600-18450800	Enhancers	Primary B cells from peripheral blood	blood
29	chr19:18450600-18450800	Enhancers	Primary T cells from cord blood	blood
30	chr19:18450600-18450800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr19:18450600-18450800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr19:18450600-18450800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr19:18450600-18450800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:18450600-18450800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:18450600-18450800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:18450600-18450800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:18450600-18450800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr19:18450600-18450800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:18450600-18450800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:18450600-18450800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:18450600-18450800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:18450600-18450800	Enhancers	Adipose Nuclei	Adipose
43	chr19:18450600-18450800	Enhancers	Brain Angular Gyrus	brain
44	chr19:18450600-18450800	Active TSS	Brain Cingulate Gyrus	brain
45	chr19:18450600-18450800	Enhancers	Brain Hippocampus Middle	brain
46	chr19:18450600-18450800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr19:18450600-18450800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:18450600-18450800	Enhancers	Brain Substantia Nigra	brain
49	chr19:18450600-18450800	Enhancers	Colonic Mucosa	Colon
50	chr19:18450600-18450800	Enhancers	Duodenum Smooth Muscle	Duodenum

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