Variant report

Variant	rs10418355
Chromosome Location	chr19:44259229-44259230
allele	A/G/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	BHLHE40	chr19:44257276-44259920	GM12878	blood:	n/a	n/a
2	EP300	chr19:44258430-44259358	HepG2	liver:	n/a	n/a
3	TAF1	chr19:44258378-44259935	ECC-1	luminal epithelium:	n/a	n/a
4	TBP	chr19:44258495-44259859	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:44259061-44259308	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:44257248-44260028	GM18951	blood:	n/a	n/a
7	STAT3	chr19:44259208-44259473	MCF10A-Er-Src	breast:	n/a	chr19:44259369-44259377 chr19:44259366-44259374
8	NRF1	chr19:44258879-44259416	H1-hESC	embryonic stem cell:	n/a	chr19:44259078-44259087 chr19:44259077-44259088 chr19:44259075-44259089 chr19:44259215-44259229 chr19:44259078-44259092 chr19:44259212-44259226 chr19:44259215-44259226 chr19:44259080-44259089 chr19:44259217-44259226 chr19:44259078-44259089
9	POLR2A	chr19:44257795-44259946	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:44258594-44259570	HepG2	liver:	n/a	n/a
11	YY1	chr19:44258711-44259340	K562	blood:	n/a	chr19:44258869-44258878
12	TAF1	chr19:44258745-44259507	GM12891	blood:	n/a	n/a
13	E2F6	chr19:44258617-44260080	H1-hESC	embryonic stem cell:	n/a	chr19:44259216-44259225 chr19:44259804-44259812 chr19:44258869-44258881 chr19:44259183-44259195 chr19:44259801-44259812 chr19:44258627-44258636 chr19:44259804-44259812 chr19:44259802-44259813 chr19:44259805-44259812 chr19:44259803-44259813 chr19:44259079-44259088 chr19:44258869-44258878 chr19:44259846-44259855
14	RCOR1	chr19:44258465-44259899	Hela-S3	cervix:	n/a	n/a
15	MAX	chr19:44258341-44259953	ECC-1	luminal epithelium:	n/a	chr19:44259184-44259194 chr19:44258867-44258877 chr19:44259784-44259793
16	TAF1	chr19:44258614-44259984	MCF-7	breast:	n/a	n/a
17	POU2F2	chr19:44257717-44259976	GM12878	blood:	n/a	chr19:44258225-44258236 chr19:44258219-44258241 chr19:44258223-44258237 chr19:44258221-44258239 chr19:44258866-44258878 chr19:44258225-44258235 chr19:44258223-44258236 chr19:44258222-44258237 chr19:44258225-44258236 chr19:44258303-44258324
18	POLR2A	chr19:44255807-44260024	GM12878	blood:	n/a	n/a
19	MYC	chr19:44258437-44259980	NB4	blood:	n/a	chr19:44259184-44259194 chr19:44258867-44258877 chr19:44259784-44259793
20	ELF1	chr19:44258622-44259383	K562	blood:	n/a	n/a
21	POLR2A	chr19:44258475-44259868	H1-neurons	neurons:	n/a	n/a
22	PML	chr19:44258420-44259934	K562	blood:	n/a	n/a
23	ELF1	chr19:44258772-44259865	A549	lung:	n/a	n/a
24	YY1	chr19:44258567-44259343	SK-N-SH_RA	brain:	n/a	chr19:44258627-44258636 chr19:44258869-44258878
25	IRF1	chr19:44258180-44259939	K562	blood:	n/a	chr19:44259664-44259676 chr19:44258598-44258612 chr19:44259253-44259273 chr19:44258868-44258882 chr19:44259661-44259675
26	SIN3AK20	chr19:44258465-44259277	K562	blood:	n/a	n/a
27	POLR2A	chr19:44258626-44259871	A549	lung:	n/a	n/a
28	NR2F2	chr19:44258462-44259260	MCF-7	breast:	n/a	n/a
29	IRF4	chr19:44258721-44259231	GM12878	blood:	n/a	n/a
30	SP1	chr19:44258243-44260044	A549	lung:	n/a	chr19:44258625-44258637 chr19:44258627-44258636 chr19:44258870-44258879 chr19:44258869-44258878 chr19:44258625-44258636 chr19:44258870-44258879 chr19:44258626-44258640 chr19:44258626-44258636 chr19:44258625-44258637 chr19:44258808-44258829 chr19:44259236-44259250 chr19:44258868-44258880 chr19:44259179-44259193 chr19:44258626-44258635 chr19:44258865-44258879
31	REST	chr19:44258741-44259826	A549	lung:	n/a	chr19:44259627-44259645 chr19:44259284-44259297
32	GTF2F1	chr19:44258765-44259787	H1-hESC	embryonic stem cell:	n/a	n/a
33	FOS	chr19:44258601-44259806	HUVEC	blood vessel:	n/a	chr19:44259409-44259420 chr19:44259182-44259191 chr19:44258817-44258826 chr19:44259204-44259216
34	MAZ	chr19:44258507-44259911	Hela-S3	cervix:	n/a	chr19:44259184-44259194 chr19:44258867-44258877 chr19:44259784-44259793
35	POLR2A	chr19:44258137-44260025	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr19:44258500-44259914	A549	lung:	n/a	n/a
37	ETS1	chr19:44258376-44259906	A549	lung:	n/a	chr19:44258867-44258878 chr19:44258691-44258702
38	TCF12	chr19:44258346-44259903	ECC-1	luminal epithelium:	n/a	n/a
39	TAF1	chr19:44258623-44259501	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr19:44258536-44260028	HUVEC	blood vessel:	n/a	n/a
41	MAX	chr19:44257748-44261049	A549	lung:	n/a	chr19:44259184-44259194 chr19:44258867-44258877 chr19:44259784-44259793
42	SIN3AK20	chr19:44258500-44259843	PANC-1	pancreas:	n/a	n/a
43	YY1	chr19:44258498-44259493	GM12891	blood:	n/a	chr19:44258627-44258636 chr19:44258869-44258878
44	CTCF	chr19:44259160-44259310	HCPEpiC	choroid plexus:	n/a	n/a
45	SPI1	chr19:44259125-44259331	K562	blood:	n/a	n/a
46	IRF1	chr19:44258154-44260024	K562	blood:	n/a	chr19:44259664-44259676 chr19:44258598-44258612 chr19:44259253-44259273 chr19:44258868-44258882 chr19:44259661-44259675
47	E2F4	chr19:44258650-44259987	Hela-S3	cervix:	n/a	chr19:44259216-44259225 chr19:44259804-44259812 chr19:44258869-44258881 chr19:44259183-44259195 chr19:44259801-44259812 chr19:44259804-44259812 chr19:44259802-44259813 chr19:44259805-44259812 chr19:44259803-44259813 chr19:44259079-44259088 chr19:44258869-44258878 chr19:44259846-44259855
48	NR3C1	chr19:44259168-44259568	ECC-1	luminal epithelium:	n/a	n/a
49	MYC	chr19:44258502-44259943	K562	blood:	n/a	chr19:44259184-44259194 chr19:44258867-44258877 chr19:44259784-44259793
50	TCF7L2	chr19:44258507-44259776	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:44259188-44259238	HCF	heart:	n/a
2	chr19:44259181-44259231	GM12891	blood:	n/a
3	chr19:44259196-44259246	NH-A	brain:	n/a
4	chr19:44259181-44259231	HL-60	blood:	n/a
5	chr19:44259188-44259238	MCF-7	breast:	n/a
6	chr19:44259196-44259246	ECC-1	luminal epithelium:	n/a
7	chr19:44259188-44259238	Jurkat	blood:	n/a
8	chr19:44259196-44259246	GM12891	blood:	n/a
9	chr19:44259188-44259238	NHDF-neo	bronchial:	n/a
10	chr19:44259181-44259231	BJ	skin:	n/a
11	chr19:44259196-44259246	H1-hESC	embryonic stem cell:	embryo
12	chr19:44259181-44259231	NT2-D1	testis:	n/a
13	chr19:44259196-44259246	HEEpiC	esophagus:	n/a
14	chr19:44259196-44259246	AG04450	lung:	fetal
15	chr19:44259188-44259238	BE2_C	brain:	n/a
16	chr19:44259196-44259246	SAEC	small airway:	n/a
17	chr19:44259181-44259231	SK-N-SH_RA	brain:	n/a
18	chr19:44259188-44259238	HCM	heart:	n/a
19	chr19:44259188-44259238	HRE	kidney:	n/a
20	chr19:44259196-44259246	HUVEC	blood vessel:	n/a
21	chr19:44259196-44259246	T-47D	breast:	n/a
22	chr19:44259196-44259246	IMR90	lung:	fetal
23	chr19:44259181-44259231	U87	brain:	n/a
24	chr19:44259196-44259246	AG04449	skin:	fetal
25	chr19:44259196-44259246	HCT-116	colon:	n/a
26	chr19:44259188-44259238	HRCEpiC	kidney:	n/a
27	chr19:44259196-44259246	SK-N-SH_RA	brain:	n/a
28	chr19:44259181-44259231	AG04449	skin:	fetal
29	chr19:44259181-44259231	AG10803	skin:	n/a
30	chr19:44259181-44259231	HCPEpiC	choroid plexus:	n/a
31	chr19:44259196-44259246	PrEC	prostate:	n/a
32	chr19:44259181-44259231	HPAEpiC	pulmonary alveolar:	n/a
33	chr19:44259188-44259238	HCT-116	colon:	n/a
34	chr19:44259188-44259238	AG10803	skin:	n/a
35	chr19:44259196-44259246	GM12892	blood:	n/a
36	chr19:44259196-44259246	HAEpiC	amniotic membrane:	n/a
37	chr19:44259181-44259231	HIPEpiC	eye:	n/a
38	chr19:44259188-44259238	HRPEpiC	eye:	n/a
39	chr19:44259188-44259238	HUVEC	blood vessel:	n/a
40	chr19:44259181-44259231	ECC-1	luminal epithelium:	n/a
41	chr19:44259188-44259238	AG04449	skin:	fetal
42	chr19:44259181-44259231	NH-A	brain:	n/a
43	chr19:44259181-44259231	LNCaP	prostate:	n/a
44	chr19:44259196-44259246	CMK	blood:	n/a
45	chr19:44259181-44259231	HNPCEpiC	eye:	n/a
46	chr19:44259188-44259238	CMK	blood:	n/a
47	chr19:44259196-44259246	LNCaP	prostate:	n/a
48	chr19:44259196-44259246	A549	lung:	n/a
49	chr19:44259188-44259238	SAEC	small airway:	n/a
50	chr19:44259196-44259246	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44100410..44103383-chr19:44259167..44262102,2	K562	blood:
2	chr19:44258963..44261252-chr2:242672884..242675015,2	MCF-7	breast:
3	chr11:62622932..62623599-chr19:44259101..44259770,2	HCT-116	colon:
4	chr19:44122148..44124570-chr19:44257332..44259810,2	K562	blood:
5	chr19:44258720..44259380-chr3:143690069..143691057,2	Hela-S3	cervix:
6	chr19:44256245..44259869-chr19:44284477..44291035,7	MCF-7	breast:
7	chr12:76952905..76954243-chr19:44258774..44259782,3	Hela-S3	cervix:
8	chr19:44121942..44125768-chr19:44258526..44260737,4	K562	blood:
9	chr18:23670769..23671301-chr19:44258757..44259743,2	Hela-S3	cervix:
10	chr19:44170992..44175159-chr19:44257509..44260839,9	K562	blood:
11	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
12	chr19:44258057..44261358-chr19:44282388..44285287,3	MCF-7	breast:
13	chr19:44256902..44259660-chr19:44715792..44718086,2	K562	blood:
14	chr19:44171504..44174584-chr19:44258221..44261397,4	MCF-7	breast:
15	chr19:44258464..44259462-chr6:27113932..27114741,2	Hela-S3	cervix:
16	chr19:44232159..44237751-chr19:44257333..44261887,5	K562	blood:
17	chr19:44172767..44174988-chr19:44257416..44259615,3	MCF-7	breast:
18	chr19:44258840..44259352-chr3:25706052..25706783,2	Hela-S3	cervix:
19	chr19:44257672..44259708-chr19:44329404..44331468,2	K562	blood:
20	chr19:33181580..33184048-chr19:44257944..44260418,2	K562	blood:
21	chr19:44258125..44259814-chr19:45145810..45147652,2	MCF-7	breast:
22	chr19:44258943..44259928-chr2:157291953..157292496,2	Hela-S3	cervix:
23	chr19:44172674..44174816-chr19:44255771..44260668,7	K562	blood:

Variant related genes	Relation type
SMG9	TF binding region
SMG9	CpG island
ENSG00000267475	Chromatin interaction
ENSG00000104783	Chromatin interaction
ENSG00000264219	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000115159	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000213965	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000141380	Chromatin interaction
ENSG00000011422	Chromatin interaction
ENSG00000131115	Chromatin interaction
ENSG00000091039	Chromatin interaction
ENSG00000077097	Chromatin interaction
ENSG00000105771	Chromatin interaction
ENSG00000180902	Chromatin interaction
ENSG00000215692	Chromatin interaction
ENSG00000181744	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000167637	Chromatin interaction
ENSG00000159871	Chromatin interaction
ENSG00000073008	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10404922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416580	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10426756	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28483837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28544228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4803656	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59204851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59800457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61676505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73565079	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44257400-44259800	Active TSS	NHDF-Ad	bronchial
2	chr19:44257400-44260200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:44257600-44259400	Active TSS	Rectal Smooth Muscle	rectum
4	chr19:44257600-44260200	Active TSS	A549	lung
5	chr19:44257800-44259400	Active TSS	Right Ventricle	heart
6	chr19:44257800-44259800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:44257800-44260200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:44257800-44260200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:44257800-44260200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:44257800-44260200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr19:44257800-44260200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:44257800-44260400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:44257800-44260600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:44258000-44259400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:44258000-44259400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:44258000-44259400	Active TSS	Hela-S3	cervix
17	chr19:44258000-44259400	Active TSS	HMEC	breast
18	chr19:44258000-44259600	Active TSS	Small Intestine	intestine
19	chr19:44258000-44259800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr19:44258000-44259800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:44258000-44259800	Active TSS	Psoas Muscle	Psoas
22	chr19:44258000-44260000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr19:44258000-44260000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:44258000-44260000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:44258000-44260200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr19:44258000-44260200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:44258000-44260400	Active TSS	GM12878-XiMat	blood
28	chr19:44258200-44259400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:44258200-44259400	Active TSS	Muscle Satellite Cultured Cells	--
30	chr19:44258200-44259400	Active TSS	Duodenum Mucosa	Duodenum
31	chr19:44258200-44259400	Active TSS	Fetal Muscle Trunk	muscle
32	chr19:44258200-44259400	Active TSS	Placenta Amnion	Placenta Amnion
33	chr19:44258200-44259400	Active TSS	Spleen	Spleen
34	chr19:44258200-44259400	Active TSS	K562	blood
35	chr19:44258200-44259400	Active TSS	Osteobl	bone
36	chr19:44258200-44259600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:44258200-44259600	Active TSS	HSMM	muscle
38	chr19:44258200-44259800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr19:44258200-44259800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:44258200-44259800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:44258200-44259800	Active TSS	Esophagus	oesophagus
42	chr19:44258200-44259800	Active TSS	Left Ventricle	heart
43	chr19:44258200-44259800	Active TSS	Lung	lung
44	chr19:44258200-44259800	Active TSS	Ovary	ovary
45	chr19:44258200-44259800	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr19:44258200-44259800	Active TSS	HSMMtube	muscle
47	chr19:44258200-44260000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:44258200-44260000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:44258200-44260000	Active TSS	Aorta	Aorta
50	chr19:44258200-44260000	Active TSS	Fetal Intestine Small	intestine

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