Variant report

Variant	rs4802210
Chromosome Location	chr19:44645748-44645749
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	CTCF	chr19:44645680-44645830	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr19:44645734-44645849	HepG2	liver:	n/a	n/a
3	HDAC2	chr19:44645466-44646015	HepG2	liver:	n/a	n/a
4	MXI1	chr19:44645264-44646079	Hela-S3	cervix:	n/a	n/a
5	JUND	chr19:44645577-44645830	K562	blood:	n/a	n/a
6	TBP	chr19:44645311-44645821	HepG2	liver:	n/a	n/a
7	HEY1	chr19:44645613-44645817	K562	blood:	n/a	n/a
8	POLR2A	chr19:44645388-44646088	MCF-7	breast:	n/a	n/a
9	STAT1	chr19:44645431-44645918	GM12878	blood:	n/a	chr19:44645854-44645862 chr19:44645678-44645692 chr19:44645681-44645689 chr19:44645681-44645704 chr19:44645675-44645695 chr19:44645675-44645695
10	ELF1	chr19:44645416-44646315	GM12878	blood:	n/a	n/a
11	MAZ	chr19:44645543-44646220	HepG2	liver:	n/a	chr19:44645968-44645978
12	MAFK	chr19:44645234-44646068	IMR90	lung:	n/a	n/a
13	REST	chr19:44645486-44645903	PFSK-1	brain:	n/a	chr19:44645551-44645564
14	MXI1	chr19:44645071-44647018	SK-N-SH	brain:	n/a	n/a
15	TAF1	chr19:44645231-44645940	A549	lung:	n/a	n/a
16	POLR2A	chr19:44645400-44645871	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:44645362-44646356	GM12878	blood:	n/a	n/a
18	SPI1	chr19:44645575-44645846	K562	blood:	n/a	chr19:44645720-44645733
19	MAFK	chr19:44645324-44646190	Hela-S3	cervix:	n/a	n/a
20	ELK1	chr19:44645123-44646121	GM12878	blood:	n/a	n/a
21	GATA3	chr19:44645439-44646318	MCF-7	breast:	n/a	chr19:44646302-44646312 chr19:44646301-44646314 chr19:44646303-44646312 chr19:44646296-44646317 chr19:44646303-44646310
22	CTCF	chr19:44645722-44645821	NHEK	skin:	n/a	n/a
23	MTA3	chr19:44645464-44645902	GM12878	blood:	n/a	n/a
24	RUNX3	chr19:44645409-44646217	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:44645356-44645990	GM12878	blood:	n/a	n/a
26	TAF1	chr19:44645386-44645863	HepG2	liver:	n/a	n/a
27	HNF4A	chr19:44645481-44645752	HepG2	liver:	n/a	n/a
28	SIX5	chr19:44645397-44645856	H1-hESC	embryonic stem cell:	n/a	chr19:44645685-44645694 chr19:44645533-44645542 chr19:44645687-44645696 chr19:44645684-44645698
29	CUX1	chr19:44645615-44645844	GM12878	blood:	n/a	n/a
30	TCF7L2	chr19:44645418-44646110	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr19:44645700-44645850	AG09309	skin:	n/a	n/a
32	POLR2A	chr19:44645362-44645989	SK-N-MC	brain:	n/a	n/a
33	STAT3	chr19:44645637-44645821	GM12878	blood:	n/a	chr19:44645678-44645692 chr19:44645679-44645690 chr19:44645681-44645689 chr19:44645681-44645704 chr19:44645675-44645695 chr19:44645675-44645695
34	CTCF	chr19:44645660-44645810	A549	lung:	n/a	n/a
35	RCOR1	chr19:44644945-44646849	IMR90	lung:	n/a	n/a
36	GABPA	chr19:44645178-44646233	SK-N-SH	brain:	n/a	n/a
37	STAT3	chr19:44645579-44645818	MCF10A-Er-Src	breast:	n/a	chr19:44645678-44645692 chr19:44645679-44645690 chr19:44645681-44645689 chr19:44645681-44645704 chr19:44645675-44645695 chr19:44645675-44645695
38	POLR2A	chr19:44645386-44645836	SK-N-SH	brain:	n/a	n/a
39	EGR1	chr19:44645597-44645888	GM12878	blood:	n/a	chr19:44645737-44645751 chr19:44645673-44645697 chr19:44645721-44645730 chr19:44645825-44645849
40	RFX5	chr19:44645473-44645853	GM12878	blood:	n/a	n/a
41	CREB1	chr19:44645352-44646123	A549	lung:	n/a	n/a
42	RUNX3	chr19:44645446-44646290	GM12878	blood:	n/a	n/a
43	NRF1	chr19:44645515-44645857	GM12878	blood:	n/a	n/a
44	MAZ	chr19:44645490-44646079	Hela-S3	cervix:	n/a	chr19:44645968-44645978
45	SIX5	chr19:44645443-44645885	GM12878	blood:	n/a	chr19:44645685-44645694 chr19:44645533-44645542 chr19:44645687-44645696 chr19:44645684-44645698
46	CTCF	chr19:44645640-44645790	HMF	breast:	n/a	n/a
47	TAF1	chr19:44645564-44645864	K562	blood:	n/a	n/a
48	TBL1XR1	chr19:44645447-44645852	GM12878	blood:	n/a	n/a
49	CTCF	chr19:44645699-44645869	GM19238	blood:	n/a	n/a
50	SPI1	chr19:44645609-44645804	K562	blood:	n/a	chr19:44645720-44645733

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:44645746-44645796	MCF-7	breast:	n/a
2	chr19:44645746-44645796	ProgFib	skin:	n/a
3	chr19:44645746-44645796	PANC-1	pancreas:	n/a
4	chr19:44645746-44645796	AG04450	lung:	fetal
5	chr19:44645715-44645765	HAEpiC	amniotic membrane:	n/a
6	chr19:44645715-44645765	GM19239	blood:	n/a
7	chr19:44645746-44645796	HRCEpiC	kidney:	n/a
8	chr19:44645715-44645765	PANC-1	pancreas:	n/a
9	chr19:44645746-44645796	RPTEC	kidney:	n/a
10	chr19:44645715-44645765	NH-A	brain:	n/a
11	chr19:44645715-44645765	HCF	heart:	n/a
12	chr19:44645746-44645796	HCPEpiC	choroid plexus:	n/a
13	chr19:44645746-44645796	SK-N-SH	brain:	n/a
14	chr19:44645746-44645796	AG09319	gingival:	n/a
15	chr19:44645746-44645796	NB4	blood:	n/a
16	chr19:44645715-44645765	HMEC	breast:	n/a
17	chr19:44645746-44645796	HAEpiC	amniotic membrane:	n/a
18	chr19:44645746-44645796	H1-hESC	embryonic stem cell:	embryo
19	chr19:44645715-44645765	HNPCEpiC	eye:	n/a
20	chr19:44645746-44645796	HPAEpiC	pulmonary alveolar:	n/a
21	chr19:44645746-44645796	Jurkat	blood:	n/a
22	chr19:44645746-44645796	SKMC	muscle:	n/a
23	chr19:44645746-44645796	NT2-D1	testis:	n/a
24	chr19:44645715-44645765	Hela-S3	cervix:	n/a
25	chr19:44645746-44645796	SK-N-MC	brain:	n/a
26	chr19:44645746-44645796	IMR90	lung:	fetal
27	chr19:44645746-44645796	GM12891	blood:	n/a
28	chr19:44645715-44645765	Jurkat	blood:	n/a
29	chr19:44645715-44645765	PrEC	prostate:	n/a
30	chr19:44645715-44645765	HUVEC	blood vessel:	n/a
31	chr19:44645715-44645765	K562	blood:	n/a
32	chr19:44645715-44645765	AG09319	gingival:	n/a
33	chr19:44645715-44645765	HRCEpiC	kidney:	n/a
34	chr19:44645746-44645796	BJ	skin:	n/a
35	chr19:44645715-44645765	AoSMC	blood vessel:	n/a
36	chr19:44645746-44645796	K562	blood:	n/a
37	chr19:44645746-44645796	ECC-1	luminal epithelium:	n/a
38	chr19:44645746-44645796	NH-A	brain:	n/a
39	chr19:44645715-44645765	NHBE	bronchial:	n/a
40	chr19:44645746-44645796	MCF10A-Er-Src	breast:	n/a
41	chr19:44645715-44645765	RPTEC	kidney:	n/a
42	chr19:44645715-44645765	HEK293	kidney:	embryo
43	chr19:44645715-44645765	LNCaP	prostate:	n/a
44	chr19:44645746-44645796	BE2_C	brain:	n/a
45	chr19:44645746-44645796	HIPEpiC	eye:	n/a
46	chr19:44645715-44645765	AG09309	skin:	n/a
47	chr19:44645746-44645796	HCF	heart:	n/a
48	chr19:44645746-44645796	GM12878	blood:	n/a
49	chr19:44645715-44645765	HEEpiC	esophagus:	n/a
50	chr19:44645746-44645796	HCT-116	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44644669..44647100-chr19:44951741..44953337,2	K562	blood:
2	chr19:44616455..44619109-chr19:44645010..44647245,2	K562	blood:
3	chr19:44596713..44600957-chr19:44644435..44647275,5	MCF-7	breast:
4	chr19:44643597..44647343-chr19:44667648..44671629,7	K562	blood:
5	chr19:44645711..44646307-chr6:26124012..26124592,2	NB4	blood:
6	chr19:44643597..44646401-chr19:44667704..44670290,3	K562	blood:
7	chr19:44616201..44619073-chr19:44644939..44647380,2	MCF-7	breast:
8	chr19:44644162..44647190-chr19:44667490..44670508,3	MCF-7	breast:

Variant related genes	Relation type
ZNF234	TF binding region
ZNF234	CpG island
ENSG00000267680	Chromatin interaction
ENSG00000167380	Chromatin interaction
ENSG00000167383	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000186019	Chromatin interaction
ENSG00000267188	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000256294	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10409155	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417451	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666199	0.83[ASN][1000 genomes]
rs11667521	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11671074	0.86[JPT][hapmap]
rs12459795	0.88[ASN][1000 genomes]
rs12460431	0.83[ASN][1000 genomes]
rs12461251	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12462557	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs12462723	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs12608984	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs12609635	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12972784	0.85[ASN][1000 genomes]
rs2051058	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2051059	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2085516	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2100643	0.87[CEU][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2125579	0.86[JPT][hapmap]
rs2279072	0.83[GIH][hapmap]
rs2279073	0.83[GIH][hapmap]
rs2293587	0.87[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2356727	0.86[ASN][1000 genomes]
rs2356751	0.87[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2356752	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3817595	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs4802209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802218	0.90[JPT][hapmap]
rs4803684	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58778698	0.90[EUR][1000 genomes]
rs60668498	0.90[EUR][1000 genomes]
rs61412562	0.90[EUR][1000 genomes]
rs61589395	0.90[EUR][1000 genomes]
rs62117771	0.90[ASN][1000 genomes]
rs6509145	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509146	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7248054	0.92[ASN][1000 genomes]
rs7249209	0.87[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7251682	0.83[GIH][hapmap]
rs7253196	0.85[ASN][1000 genomes]
rs7508523	0.81[ASN][1000 genomes]
rs8103838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8105073	0.85[JPT][hapmap]
rs8105479	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8108934	0.86[ASN][1000 genomes]
rs9646643	0.82[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4802210	SIGLEC9	cis	parietal	SCAN
rs4802210	GPR77	cis	cerebellum	SCAN
rs4802210	DHDH	cis	parietal	SCAN
rs4802210	AP2S1	cis	cerebellum	SCAN
rs4802210	APOC1	cis	parietal	SCAN
rs4802210	NOSIP	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44644200-44646600	Active TSS	Colon Smooth Muscle	Colon
2	chr19:44644600-44646200	Active TSS	Right Ventricle	heart
3	chr19:44644800-44646200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr19:44644800-44646400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:44644800-44646400	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr19:44644800-44646400	Active TSS	GM12878-XiMat	blood
7	chr19:44644800-44646600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:44644800-44646600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:44644800-44646600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr19:44644800-44646600	Active TSS	Psoas Muscle	Psoas
11	chr19:44644800-44646800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr19:44644800-44646800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:44644800-44646800	Active TSS	Fetal Intestine Small	intestine
14	chr19:44644800-44647000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr19:44644800-44647000	Active TSS	HSMMtube	muscle
16	chr19:44644800-44647400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:44645000-44646200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:44645000-44646200	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:44645000-44646400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:44645000-44646400	Active TSS	Brain Substantia Nigra	brain
21	chr19:44645000-44646600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr19:44645000-44646600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:44645000-44646600	Active TSS	Esophagus	oesophagus
24	chr19:44645000-44646600	Active TSS	Hela-S3	cervix
25	chr19:44645000-44646600	Bivalent/Poised TSS	HepG2	liver
26	chr19:44645000-44646800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:44645000-44646800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:44645000-44646800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:44645000-44646800	Active TSS	Colonic Mucosa	Colon
30	chr19:44645000-44646800	Active TSS	Fetal Muscle Trunk	muscle
31	chr19:44645000-44646800	Active TSS	Ovary	ovary
32	chr19:44645000-44647000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:44645000-44647000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr19:44645000-44647000	Active TSS	NHDF-Ad	bronchial
35	chr19:44645200-44645800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:44645200-44646200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:44645200-44646200	Active TSS	Brain Angular Gyrus	brain
38	chr19:44645200-44646200	Active TSS	Fetal Brain Male	brain
39	chr19:44645200-44646200	Active TSS	Fetal Brain Female	brain
40	chr19:44645200-44646200	Active TSS	Fetal Heart	heart
41	chr19:44645200-44646200	Active TSS	NHEK	skin
42	chr19:44645200-44646400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr19:44645200-44646400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:44645200-44646600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr19:44645200-44646600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:44645200-44646600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:44645200-44646600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:44645200-44646600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:44645200-44646600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:44645200-44646600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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