Variant report

Variant	rs7253360
Chromosome Location	chr19:38717264-38717265
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	RAD21	chr19:38716792-38717291	A549	lung:	n/a	chr19:38717025-38717044 chr19:38717030-38717040 chr19:38717028-38717041
2	CTCF	chr19:38716753-38717281	MCF-7	breast:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
3	CTCF	chr19:38717259-38717387	NHEK	skin:	n/a	n/a
4	CTCF	chr19:38717220-38717370	GM12867	blood:	n/a	n/a
5	TCF12	chr19:38716891-38717277	A549	lung:	n/a	n/a
6	RCOR1	chr19:38716876-38717355	K562	blood:	n/a	n/a
7	CTCF	chr19:38716663-38717425	GM12892	blood:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
8	SIN3AK20	chr19:38716933-38717471	A549	lung:	n/a	n/a
9	CTCF	chr19:38717240-38717390	WERI-Rb-1	eye:	n/a	n/a
10	CTCF	chr19:38716655-38717300	IMR90	lung:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
11	BCL3	chr19:38716873-38717411	A549	lung:	n/a	n/a
12	SP1	chr19:38716864-38717289	H1-hESC	embryonic stem cell:	n/a	chr19:38717004-38717014 chr19:38717004-38717014
13	TCF12	chr19:38716904-38717631	A549	lung:	n/a	n/a
14	CTCF	chr19:38717200-38717350	GM12868	blood:	n/a	n/a
15	CTCF	chr19:38716543-38717543	SK-N-SH	brain:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
16	CTCF	chr19:38716905-38717328	K562	blood:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
17	MAX	chr19:38716965-38717448	K562	blood:	n/a	n/a
18	CTCF	chr19:38717248-38717332	GM19239	blood:	n/a	n/a
19	CTCF	chr19:38717260-38717410	NHLF	lung:	n/a	n/a
20	SMC3	chr19:38716868-38717497	SK-N-SH	brain:	n/a	chr19:38717026-38717040 chr19:38717030-38717040
21	CTCF	chr19:38717260-38717410	AG10803	skin:	n/a	n/a
22	CTCF	chr19:38716772-38717277	A549	lung:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
23	CTCF	chr19:38716420-38717760	A549	lung:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
24	RAD21	chr19:38716774-38717297	ECC-1	luminal epithelium:	n/a	chr19:38717025-38717044 chr19:38717030-38717040 chr19:38717028-38717041
25	CTCF	chr19:38717225-38717400	GM12891	blood:	n/a	n/a
26	CTCF	chr19:38716834-38717400	GM19238	blood:	n/a	chr19:38717027-38717036 chr19:38717029-38717039 chr19:38717024-38717042 chr19:38717027-38717040 chr19:38717026-38717047 chr19:38717180-38717188 chr19:38717025-38717041 chr19:38717027-38717040
27	CTCF	chr19:38717221-38717377	GM19240	blood:	n/a	n/a
28	SIN3A	chr19:38716901-38717461	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr19:38717210-38717307	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr19:38716907-38717377	HCT-116	colon:	n/a	chr19:38717025-38717044 chr19:38717030-38717040 chr19:38717028-38717041
31	RAD21	chr19:38716894-38717267	H1-hESC	embryonic stem cell:	n/a	chr19:38717025-38717044 chr19:38717030-38717040 chr19:38717028-38717041
32	TBP	chr19:38716926-38717373	K562	blood:	n/a	n/a
33	ELK1	chr19:38717262-38717278	K562	blood:	n/a	n/a
34	CTCF	chr19:38717260-38717410	GM12866	blood:	n/a	n/a
35	RAD21	chr19:38716776-38717339	A549	lung:	n/a	chr19:38717025-38717044 chr19:38717030-38717040 chr19:38717028-38717041

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38717239-38717289	HMEC	breast:	n/a
2	chr19:38717239-38717289	T-47D	breast:	n/a
3	chr19:38717239-38717289	PANC-1	pancreas:	n/a
4	chr19:38717239-38717289	ovcar-3	ovarian:	n/a
5	chr19:38717239-38717289	NT2-D1	testis:	n/a
6	chr19:38717239-38717289	IMR90	lung:	fetal
7	chr19:38717239-38717289	HPAEpiC	pulmonary alveolar:	n/a
8	chr19:38717239-38717289	NHBE	bronchial:	n/a
9	chr19:38717239-38717289	H1-hESC	embryonic stem cell:	embryo
10	chr19:38717239-38717289	MCF-7	breast:	n/a
11	chr19:38717239-38717289	U87	brain:	n/a
12	chr19:38717239-38717289	MCF10A-Er-Src	breast:	n/a
13	chr19:38717239-38717289	GM12891	blood:	n/a
14	chr19:38717239-38717289	GM12878	blood:	n/a
15	chr19:38717239-38717289	GM12892	blood:	n/a
16	chr19:38717239-38717289	HRE	kidney:	n/a
17	chr19:38717239-38717289	NHDF-neo	bronchial:	n/a
18	chr19:38717239-38717289	HRCEpiC	kidney:	n/a
19	chr19:38717239-38717289	HNPCEpiC	eye:	n/a
20	chr19:38717239-38717289	HIPEpiC	eye:	n/a
21	chr19:38717239-38717289	HEEpiC	esophagus:	n/a
22	chr19:38717239-38717289	Caco-2	colon:	n/a
23	chr19:38717239-38717289	CMK	blood:	n/a
24	chr19:38717239-38717289	HAEpiC	amniotic membrane:	n/a
25	chr19:38717239-38717289	HepG2	liver:	n/a
26	chr19:38717239-38717289	SK-N-MC	brain:	n/a
27	chr19:38717239-38717289	HCM	heart:	n/a
28	chr19:38717239-38717289	LNCaP	prostate:	n/a
29	chr19:38717239-38717289	BE2_C	brain:	n/a
30	chr19:38717239-38717289	PrEC	prostate:	n/a
31	chr19:38717239-38717289	SAEC	small airway:	n/a
32	chr19:38717239-38717289	HCF	heart:	n/a
33	chr19:38717239-38717289	AoSMC	blood vessel:	n/a
34	chr19:38717239-38717289	SK-N-SH_RA	brain:	n/a
35	chr19:38717239-38717289	HUVEC	blood vessel:	n/a
36	chr19:38717239-38717289	Hepatocyte	liver:	n/a
37	chr19:38717239-38717289	HL-60	blood:	n/a
38	chr19:38717239-38717289	AG04449	skin:	fetal
39	chr19:38717239-38717289	HCT-116	colon:	n/a
40	chr19:38717239-38717289	Hela-S3	cervix:	n/a
41	chr19:38717239-38717289	ProgFib	skin:	n/a
42	chr19:38717239-38717289	GM19239	blood:	n/a
43	chr19:38717239-38717289	HRPEpiC	eye:	n/a
44	chr19:38717239-38717289	AG09319	gingival:	n/a
45	chr19:38717239-38717289	SKMC	muscle:	n/a
46	chr19:38717239-38717289	NB4	blood:	n/a
47	chr19:38717239-38717289	AG04450	lung:	fetal
48	chr19:38717239-38717289	Jurkat	blood:	n/a
49	chr19:38717239-38717289	HEK293	kidney:	embryo
50	chr19:38717239-38717289	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38717093..38718677-chr19:38724126..38726976,2	K562	blood:
2	chr19:38716611..38717479-chr19:38825815..38826777,3	K562	blood:
3	chr19:38717014..38717887-chr19:38825862..38826722,3	MCF-7	breast:
4	chr19:38715204..38718579-chr19:38826351..38828588,3	K562	blood:
5	chr19:38713729..38715323-chr19:38716058..38719030,2	K562	blood:
6	chr19:38715242..38718088-chr19:38941035..38943575,2	K562	blood:
7	chr19:38716917..38718796-chr19:38722935..38725683,2	MCF-7	breast:
8	chr19:38651241..38653210-chr19:38716095..38718461,3	K562	blood:
9	chr19:38715608..38719883-chr19:38825304..38828918,6	K562	blood:
10	chr19:38651349..38653210-chr19:38716095..38718461,2	K562	blood:

Variant related genes	Relation type
DPF1	TF binding region
DPF1	CpG island
ENSG00000011332	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2384781	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60328056	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7253473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256364	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8108197	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109991	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7253360	SPINT2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38715200-38718200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:38715200-38719000	Weak transcription	Right Atrium	heart
3	chr19:38715200-38719200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:38715200-38719200	Weak transcription	Pancreas	Pancrea
5	chr19:38715400-38718200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:38715400-38718200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:38715400-38718400	Weak transcription	Brain Angular Gyrus	brain
8	chr19:38715400-38718400	Weak transcription	Fetal Heart	heart
9	chr19:38715400-38718600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:38715400-38719000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:38715400-38719200	Weak transcription	NH-A	brain
12	chr19:38715400-38719200	Weak transcription	NHDF-Ad	bronchial
13	chr19:38715600-38718000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:38715600-38718000	Weak transcription	NHEK	skin
15	chr19:38715600-38719400	Weak transcription	Brain Anterior Caudate	brain
16	chr19:38715600-38719600	Weak transcription	Hela-S3	cervix
17	chr19:38716000-38717600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr19:38716600-38717400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:38716600-38718000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr19:38716600-38718000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:38716600-38718400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr19:38716600-38718600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:38716600-38719200	Enhancers	A549	lung
24	chr19:38716600-38720800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr19:38716800-38718600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:38716800-38719200	Enhancers	Fetal Brain Male	brain
27	chr19:38717000-38717400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:38717000-38717400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr19:38717000-38717400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
30	chr19:38717000-38717400	Enhancers	Brain Cingulate Gyrus	brain
31	chr19:38717000-38717400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr19:38717000-38717400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr19:38717000-38717400	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr19:38717000-38718000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr19:38717000-38718800	Flanking Active TSS	Fetal Brain Female	brain
36	chr19:38717200-38717400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
37	chr19:38717200-38717400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:38717200-38717400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
39	chr19:38717200-38717400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:38717200-38717400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
41	chr19:38717200-38717400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:38717200-38717400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
43	chr19:38717200-38717400	Flanking Active TSS	K562	blood
44	chr19:38717200-38717600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:38717200-38717600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
46	chr19:38717200-38717600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:38717200-38717600	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr19:38717200-38717600	Bivalent Enhancer	HUVEC	blood vessel
49	chr19:38717200-38718200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:38717200-38718600	Enhancers	Cortex derived primary cultured neurospheres	brain

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