Variant report

Variant	rs1664696
Chromosome Location	chr19:37701574-37701575
allele	C/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	CTCF	chr19:37701480-37701630	HCM	heart:	n/a	n/a
2	POLR2A	chr19:37701225-37701691	Hela-S3	cervix:	n/a	n/a
3	TBP	chr19:37701106-37701796	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF384	chr19:37701404-37701708	K562	blood:	n/a	n/a
5	ELF1	chr19:37701167-37701687	HepG2	liver:	n/a	chr19:37701426-37701439
6	CTCF	chr19:37701480-37701725	Kidney_OC	kidney:	n/a	n/a
7	ATF1	chr19:37701117-37701741	K562	blood:	n/a	n/a
8	CTCF	chr19:37701560-37701710	HBMEC	blood vessel:	n/a	n/a
9	BACH1	chr19:37701264-37701663	K562	blood:	n/a	n/a
10	ZNF263	chr19:37701186-37701889	HEK293-T-REx	kidney:	n/a	n/a
11	SRF	chr19:37701148-37701727	MCF-7	breast:	n/a	n/a
12	CTCF	chr19:37701560-37701710	HMEC	breast:	n/a	n/a
13	POLR2A	chr19:37701243-37701764	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr19:37701540-37701690	HPF	lung:	n/a	n/a
15	POLR2A	chr19:37701115-37701779	GM12878	blood:	n/a	n/a
16	ELK1	chr19:37701312-37701609	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:37701171-37701788	MCF-7	breast:	n/a	n/a
18	CTCF	chr19:37701540-37701690	BJ	skin:	n/a	n/a
19	GABPA	chr19:37701205-37701627	H1-hESC	embryonic stem cell:	n/a	chr19:37701474-37701485 chr19:37701471-37701485
20	MAX	chr19:37701126-37701800	A549	lung:	n/a	n/a
21	TCF7L2	chr19:37701479-37701723	MCF-7	breast:	n/a	chr19:37701625-37701639
22	TAF1	chr19:37701169-37701889	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:37701185-37701788	K562	blood:	n/a	n/a
24	MAZ	chr19:37701096-37701779	GM12878	blood:	n/a	n/a
25	GABPA	chr19:37700931-37701749	A549	lung:	n/a	chr19:37701474-37701485 chr19:37701471-37701485
26	FOXA1	chr19:37701291-37701778	T-47D	breast:	n/a	chr19:37701512-37701527
27	POLR2A	chr19:37701198-37701678	GM12878	blood:	n/a	n/a
28	STAT3	chr19:37701374-37701739	MCF10A-Er-Src	breast:	n/a	n/a
29	CREB1	chr19:37701184-37701770	HepG2	liver:	n/a	n/a
30	CREB1	chr19:37701083-37701713	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr19:37701324-37701853	HepG2	liver:	n/a	chr19:37701624-37701632 chr19:37701621-37701643 chr19:37701621-37701631 chr19:37701619-37701636 chr19:37701620-37701636
32	YY1	chr19:37701086-37701860	SK-N-SH_RA	brain:	n/a	chr19:37701624-37701632 chr19:37701621-37701643 chr19:37701621-37701631 chr19:37701619-37701636 chr19:37701620-37701636
33	CTCF	chr19:37701345-37701833	GM12878	blood:	n/a	n/a
34	UBTF	chr19:37701399-37701634	K562	blood:	n/a	n/a
35	TAL1	chr19:37701383-37701707	K562	blood:	n/a	n/a
36	YY1	chr19:37700976-37702078	SK-N-SH	brain:	n/a	chr19:37701624-37701632 chr19:37701621-37701643 chr19:37701621-37701631 chr19:37701619-37701636 chr19:37701620-37701636
37	TAF1	chr19:37701336-37701646	K562	blood:	n/a	n/a
38	SIN3A	chr19:37701211-37701698	GM12878	blood:	n/a	n/a
39	STAT3	chr19:37701385-37701741	MCF10A-Er-Src	breast:	n/a	n/a
40	TCF7L2	chr19:37701388-37701761	PANC-1	pancreas:	n/a	chr19:37701625-37701639
41	STAT3	chr19:37701384-37701741	MCF10A-Er-Src	breast:	n/a	n/a
42	SP1	chr19:37701265-37701745	GM12878	blood:	n/a	n/a
43	CTCF	chr19:37701478-37701795	IMR90	lung:	n/a	n/a
44	CEBPB	chr19:37701333-37701733	K562	blood:	n/a	n/a
45	PAX5	chr19:37701315-37701644	GM12878	blood:	n/a	n/a
46	ZKSCAN1	chr19:37701246-37701704	Hela-S3	cervix:	n/a	n/a
47	YY1	chr19:37701095-37701782	GM12892	blood:	n/a	chr19:37701624-37701632 chr19:37701621-37701643 chr19:37701621-37701631 chr19:37701619-37701636 chr19:37701620-37701636
48	POLR2A	chr19:37701097-37701620	HUVEC	blood vessel:	n/a	n/a
49	GABPA	chr19:37701000-37701889	SK-N-SH	brain:	n/a	chr19:37701474-37701485 chr19:37701471-37701485
50	STAT3	chr19:37701406-37701741	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:37701550-37701600	AoSMC	blood vessel:	n/a
2	chr19:37701550-37701600	HRCEpiC	kidney:	n/a
3	chr19:37701550-37701600	HRPEpiC	eye:	n/a
4	chr19:37701550-37701600	GM12892	blood:	n/a
5	chr19:37701550-37701600	U87	brain:	n/a
6	chr19:37701550-37701600	ovcar-3	ovarian:	n/a
7	chr19:37701550-37701600	HAEpiC	amniotic membrane:	n/a
8	chr19:37701550-37701600	PANC-1	pancreas:	n/a
9	chr19:37701550-37701600	A549	lung:	n/a
10	chr19:37701550-37701600	CMK	blood:	n/a
11	chr19:37701550-37701600	HCPEpiC	choroid plexus:	n/a
12	chr19:37701550-37701600	NB4	blood:	n/a
13	chr19:37701550-37701600	BE2_C	brain:	n/a
14	chr19:37701550-37701600	HPAEpiC	pulmonary alveolar:	n/a
15	chr19:37701550-37701600	AG04449	skin:	fetal
16	chr19:37701550-37701600	H1-hESC	embryonic stem cell:	embryo
17	chr19:37701550-37701600	SAEC	small airway:	n/a
18	chr19:37701550-37701600	GM12878	blood:	n/a
19	chr19:37701550-37701600	NHBE	bronchial:	n/a
20	chr19:37701550-37701600	Caco-2	colon:	n/a
21	chr19:37701550-37701600	SK-N-SH	brain:	n/a
22	chr19:37701550-37701600	ProgFib	skin:	n/a
23	chr19:37701550-37701600	LNCaP	prostate:	n/a
24	chr19:37701550-37701600	AG09309	skin:	n/a
25	chr19:37701550-37701600	SK-N-MC	brain:	n/a
26	chr19:37701550-37701600	HNPCEpiC	eye:	n/a
27	chr19:37701550-37701600	HCT-116	colon:	n/a
28	chr19:37701550-37701600	BJ	skin:	n/a
29	chr19:37701550-37701600	HUVEC	blood vessel:	n/a
30	chr19:37701550-37701600	HIPEpiC	eye:	n/a
31	chr19:37701550-37701600	T-47D	breast:	n/a
32	chr19:37701550-37701600	NT2-D1	testis:	n/a
33	chr19:37701550-37701600	GM12891	blood:	n/a
34	chr19:37701550-37701600	AG04450	lung:	fetal
35	chr19:37701550-37701600	SKMC	muscle:	n/a
36	chr19:37701550-37701600	PFSK-1	brain:	n/a
37	chr19:37701550-37701600	Hela-S3	cervix:	n/a
38	chr19:37701550-37701600	ECC-1	luminal epithelium:	n/a
39	chr19:37701550-37701600	GM19239	blood:	n/a
40	chr19:37701550-37701600	HMEC	breast:	n/a
41	chr19:37701550-37701600	GM06990	blood:	n/a
42	chr19:37701550-37701600	HL-60	blood:	n/a
43	chr19:37701550-37701600	HCF	heart:	n/a
44	chr19:37701550-37701600	AG10803	skin:	n/a
45	chr19:37701550-37701600	SK-N-SH_RA	brain:	n/a
46	chr19:37701550-37701600	MCF-7	breast:	n/a
47	chr19:37701550-37701600	NHDF-neo	bronchial:	n/a
48	chr19:37701550-37701600	NH-A	brain:	n/a
49	chr19:37701550-37701600	K562	blood:	n/a
50	chr19:37701550-37701600	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150898231..150898792-chr19:37701107..37701818,2	HCT-116	colon:
2	chr17:56734971..56737597-chr19:37700185..37703092,2	MCF-7	breast:
3	chr19:37700159..37703141-chr19:37808841..37810702,2	MCF-7	breast:
4	chr19:37700501..37704644-chr19:37706690..37710773,7	K562	blood:
5	chr19:37699969..37703002-chr19:37707384..37710417,4	MCF-7	breast:
6	chr19:37699250..37701731-chr19:37707688..37710566,5	MCF-7	breast:

Variant related genes	Relation type
ZNF585B	TF binding region
ENSG00000267360	TF binding region
ZNF585B	CpG island
ENSG00000267360	CpG island
ENSG00000245680	Chromatin interaction
ENSG00000188283	Chromatin interaction
ENSG00000181666	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10402144	0.94[EUR][1000 genomes]
rs10411236	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1234257	0.92[EUR][1000 genomes]
rs1234259	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1234260	0.81[ASN][1000 genomes]
rs12459637	0.85[JPT][hapmap]
rs1657506	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs172786	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188877	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28613334	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs320877	0.91[EUR][1000 genomes]
rs320879	0.96[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs320889	0.98[EUR][1000 genomes]
rs320891	1.00[CEU][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes]
rs8108727	0.81[YRI][hapmap]
rs860386	0.96[CEU][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1664696	SSBP2	cis	Temporal Cortex	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37700400-37701800	Active TSS	NHDF-Ad	bronchial
2	chr19:37700400-37702000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:37700400-37702200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:37700400-37702200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:37700400-37702200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:37700400-37702200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:37700400-37702200	Active TSS	Primary T cells from cord blood	blood
8	chr19:37700400-37702200	Active TSS	K562	blood
9	chr19:37700400-37702400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr19:37700600-37701800	Active TSS	Adipose Nuclei	Adipose
11	chr19:37700600-37701800	Active TSS	Fetal Brain Female	brain
12	chr19:37700600-37702000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:37700600-37702000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:37700600-37702000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:37700600-37702000	Active TSS	Colonic Mucosa	Colon
16	chr19:37700600-37702000	Active TSS	Fetal Intestine Small	intestine
17	chr19:37700600-37702000	Active TSS	Right Ventricle	heart
18	chr19:37700600-37702200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:37700600-37702200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:37700600-37702200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:37700600-37702200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:37700600-37702200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:37700600-37702400	Active TSS	Duodenum Mucosa	Duodenum
24	chr19:37700600-37702400	Active TSS	HMEC	breast
25	chr19:37700800-37701600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:37700800-37701600	Active TSS	Brain Anterior Caudate	brain
27	chr19:37700800-37701800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr19:37700800-37701800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:37700800-37701800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:37700800-37701800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:37700800-37701800	Active TSS	Fetal Muscle Trunk	muscle
32	chr19:37700800-37701800	Active TSS	Fetal Muscle Leg	muscle
33	chr19:37700800-37701800	Active TSS	Pancreas	Pancrea
34	chr19:37700800-37701800	Active TSS	HSMMtube	muscle
35	chr19:37700800-37701800	Active TSS	NHLF	lung
36	chr19:37700800-37702000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr19:37700800-37702000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr19:37700800-37702000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:37700800-37702000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:37700800-37702000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:37700800-37702000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr19:37700800-37702000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:37700800-37702000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr19:37700800-37702000	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr19:37700800-37702000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:37700800-37702000	Active TSS	Brain Angular Gyrus	brain
47	chr19:37700800-37702000	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:37700800-37702000	Active TSS	Fetal Intestine Large	intestine
49	chr19:37700800-37702000	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr19:37700800-37702000	Active TSS	Fetal Lung	lung

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