Variant report

Variant	rs74131448
Chromosome Location	chr10:52384913-52384914
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	POLR2A	chr10:52383364-52385552	GM12878	blood:	n/a	n/a
2	FOXA1	chr10:52384840-52385364	HepG2	liver:	n/a	chr10:52385176-52385188
3	ELF1	chr10:52382439-52385283	GM12878	blood:	n/a	chr10:52385128-52385140 chr10:52384980-52384989
4	MAX	chr10:52383421-52385509	ECC-1	luminal epithelium:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
5	YY1	chr10:52384162-52385584	SK-N-SH_RA	brain:	n/a	chr10:52385126-52385135 chr10:52384570-52384584 chr10:52385126-52385137
6	MAX	chr10:52383402-52385378	SK-N-SH	brain:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
7	SP1	chr10:52383337-52385386	HCT-116	colon:	n/a	chr10:52384344-52384356 chr10:52384344-52384356 chr10:52384345-52384354 chr10:52385059-52385072 chr10:52384346-52384355 chr10:52383448-52383457 chr10:52384345-52384354
8	ELF1	chr10:52384109-52385190	HepG2	liver:	n/a	chr10:52385128-52385140 chr10:52384980-52384989
9	MAFK	chr10:52383950-52385790	K562	blood:	n/a	n/a
10	PBX3	chr10:52384115-52385332	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr10:52383429-52385947	K562	blood:	n/a	n/a
12	POLR2A	chr10:52384184-52385177	A549	lung:	n/a	n/a
13	POLR2A	chr10:52383376-52385992	U87	brain:	n/a	n/a
14	FOXM1	chr10:52384687-52385515	GM12878	blood:	n/a	n/a
15	TAF1	chr10:52384181-52385183	HepG2	liver:	n/a	n/a
16	EBF1	chr10:52384871-52385352	GM12878	blood:	n/a	chr10:52385203-52385212 chr10:52385202-52385212 chr10:52385201-52385214
17	MAX	chr10:52383304-52385178	HUVEC	blood vessel:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
18	USF1	chr10:52384207-52385539	SK-N-SH	brain:	n/a	chr10:52384828-52384844 chr10:52384677-52384688 chr10:52385126-52385142
19	POLR2A	chr10:52381694-52385975	Hela-S3	cervix:	n/a	n/a
20	RCOR1	chr10:52383404-52385746	K562	blood:	n/a	n/a
21	MXI1	chr10:52381308-52386209	SK-N-SH	brain:	n/a	chr10:52384448-52384457 chr10:52384446-52384455
22	GABPA	chr10:52384151-52385306	HL-60	blood:	n/a	chr10:52384430-52384441 chr10:52384430-52384444 chr10:52384427-52384441
23	POLR2A	chr10:52383148-52385231	A549	lung:	n/a	n/a
24	THAP1	chr10:52384202-52384971	K562	blood:	n/a	n/a
25	YY1	chr10:52384264-52385186	HepG2	liver:	n/a	chr10:52385126-52385135 chr10:52384570-52384584 chr10:52385126-52385137
26	SIX5	chr10:52384799-52385544	A549	lung:	n/a	n/a
27	POLR2A	chr10:52383216-52385848	GM12892	blood:	n/a	n/a
28	MAX	chr10:52382912-52385590	A549	lung:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
29	E2F6	chr10:52383388-52385165	H1-hESC	embryonic stem cell:	n/a	chr10:52383483-52383493 chr10:52384118-52384132 chr10:52383640-52383649 chr10:52384541-52384553
30	MAZ	chr10:52382568-52385628	Hela-S3	cervix:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
31	IRF1	chr10:52383560-52385932	K562	blood:	n/a	chr10:52383896-52383910 chr10:52384342-52384356 chr10:52385614-52385630 chr10:52384250-52384264
32	ZNF143	chr10:52384097-52385218	Hela-S3	cervix:	n/a	n/a
33	EBF1	chr10:52383564-52385457	GM12878	blood:	n/a	chr10:52385203-52385212 chr10:52384007-52384020 chr10:52384009-52384018 chr10:52385202-52385212 chr10:52385201-52385214 chr10:52384008-52384019
34	TAF1	chr10:52384049-52385408	K562	blood:	n/a	n/a
35	RELA	chr10:52382955-52385813	GM15510	blood:	n/a	n/a
36	YY1	chr10:52383861-52385476	H1-hESC	embryonic stem cell:	n/a	chr10:52385126-52385135 chr10:52384570-52384584 chr10:52385126-52385137 chr10:52384015-52384026
37	POLR2A	chr10:52384181-52385165	HepG2	liver:	n/a	n/a
38	ATF1	chr10:52384112-52385291	K562	blood:	n/a	n/a
39	MYC	chr10:52384216-52385180	HepG2	liver:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
40	POLR2A	chr10:52384085-52385141	SK-N-SH	brain:	n/a	n/a
41	TRIM28	chr10:52384001-52385815	K562	blood:	n/a	chr10:52385807-52385815 chr10:52385790-52385798
42	MXI1	chr10:52383092-52385294	HepG2	liver:	n/a	chr10:52384448-52384457 chr10:52384446-52384455
43	EP300	chr10:52383747-52385832	K562	blood:	n/a	chr10:52384373-52384389 chr10:52385763-52385776 chr10:52384377-52384393 chr10:52384821-52384837
44	SMC3	chr10:52383850-52385362	GM12878	blood:	n/a	chr10:52385136-52385144 chr10:52385130-52385140 chr10:52385130-52385144
45	SP1	chr10:52383479-52385303	K562	blood:	n/a	chr10:52384344-52384356 chr10:52384344-52384356 chr10:52384345-52384354 chr10:52385059-52385072 chr10:52384346-52384355 chr10:52384345-52384354
46	EP300	chr10:52384853-52385755	GM12878	blood:	n/a	n/a
47	JUN	chr10:52383103-52385367	K562	blood:	n/a	chr10:52384395-52384409 chr10:52384342-52384351 chr10:52384347-52384356
48	ELK1	chr10:52384791-52385100	GM12878	blood:	n/a	n/a
49	TAF7	chr10:52383934-52385829	H1-hESC	embryonic stem cell:	n/a	n/a
50	FOXA2	chr10:52384276-52385055	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:52384903-52384953	PFSK-1	brain:	n/a
2	chr10:52384903-52384953	HL-60	blood:	n/a
3	chr10:52384903-52384953	SK-N-SH	brain:	n/a
4	chr10:52384903-52384953	NB4	blood:	n/a
5	chr10:52384903-52384953	MCF-7	breast:	n/a
6	chr10:52384903-52384953	GM06990	blood:	n/a
7	chr10:52384903-52384953	Hepatocyte	liver:	n/a
8	chr10:52384903-52384953	IMR90	lung:	fetal
9	chr10:52384903-52384953	AG09309	skin:	n/a
10	chr10:52384903-52384953	HEK293	kidney:	embryo
11	chr10:52384903-52384953	K562	blood:	n/a
12	chr10:52384903-52384953	BE2_C	brain:	n/a
13	chr10:52384903-52384953	CMK	blood:	n/a
14	chr10:52384903-52384953	NH-A	brain:	n/a
15	chr10:52384903-52384953	AoSMC	blood vessel:	n/a
16	chr10:52384903-52384953	AG09319	gingival:	n/a
17	chr10:52384903-52384953	HCF	heart:	n/a
18	chr10:52384903-52384953	NHBE	bronchial:	n/a
19	chr10:52384903-52384953	BJ	skin:	n/a
20	chr10:52384903-52384953	NT2-D1	testis:	n/a
21	chr10:52384903-52384953	HMEC	breast:	n/a
22	chr10:52384903-52384953	HCM	heart:	n/a
23	chr10:52384903-52384953	HRE	kidney:	n/a
24	chr10:52384903-52384953	Caco-2	colon:	n/a
25	chr10:52384903-52384953	ECC-1	luminal epithelium:	n/a
26	chr10:52384903-52384953	GM12878	blood:	n/a
27	chr10:52384903-52384953	PANC-1	pancreas:	n/a
28	chr10:52384903-52384953	HAEpiC	amniotic membrane:	n/a
29	chr10:52384903-52384953	U87	brain:	n/a
30	chr10:52384903-52384953	AG04449	skin:	fetal
31	chr10:52384903-52384953	ProgFib	skin:	n/a
32	chr10:52384903-52384953	LNCaP	prostate:	n/a
33	chr10:52384903-52384953	AG04450	lung:	fetal
34	chr10:52384903-52384953	A549	lung:	n/a
35	chr10:52384903-52384953	SK-N-MC	brain:	n/a
36	chr10:52384903-52384953	GM12892	blood:	n/a
37	chr10:52384903-52384953	HCPEpiC	choroid plexus:	n/a
38	chr10:52384903-52384953	SK-N-SH_RA	brain:	n/a
39	chr10:52384903-52384953	SAEC	small airway:	n/a
40	chr10:52384903-52384953	MCF10A-Er-Src	breast:	n/a
41	chr10:52384903-52384953	Jurkat	blood:	n/a
42	chr10:52384903-52384953	HPAEpiC	pulmonary alveolar:	n/a
43	chr10:52384903-52384953	NHDF-neo	bronchial:	n/a
44	chr10:52384903-52384953	HRPEpiC	eye:	n/a
45	chr10:52384903-52384953	HUVEC	blood vessel:	n/a
46	chr10:52384903-52384953	RPTEC	kidney:	n/a
47	chr10:52384903-52384953	HepG2	liver:	n/a
48	chr10:52384903-52384953	HIPEpiC	eye:	n/a
49	chr10:52384903-52384953	PrEC	prostate:	n/a
50	chr10:52384903-52384953	T-47D	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
2	chr10:52384532..52385151-chr14:35451145..35451802,2	Hela-S3	cervix:
3	chr10:52384254..52384940-chr8:11659944..11660800,2	NB4	blood:
4	chr10:52342227..52348125-chr10:52381237..52386507,8	K562	blood:
5	chr10:52341787..52346100-chr10:52382899..52385718,8	MCF-7	breast:
6	chr10:52381243..52386496-chr10:52418227..52421959,6	MCF-7	breast:
7	chr10:52382538..52386733-chr10:52497918..52501112,4	MCF-7	breast:
8	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
9	chr10:52103151..52105270-chr10:52383748..52386662,2	K562	blood:
10	chr10:52365691..52371767-chr10:52381261..52385919,7	K562	blood:
11	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
12	chr1:249131869..249132502-chr10:52384457..52385367,2	Hela-S3	cervix:
13	chr10:52343887..52348125-chr10:52383719..52386062,5	K562	blood:
14	chr10:52229968..52233210-chr10:52382214..52385931,3	MCF-7	breast:
15	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASAH2B-2	chr10:52383739-52386623	NONHSAT013388
2	lnc-ASAH2B-2	chr10:52384711-52384951	ENSG00000226200.2
3	lnc-ASAH2B-2	chr10:52384723-52384951	ENSG00000226200.2

Variant related genes	Relation type
SGMS1	TF binding region
SGMS1	CpG island
ENSG00000258704	Chromatin interaction
ENSG00000251950	Chromatin interaction
ENSG00000204147	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000100883	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000230036	Chromatin interaction
ENSG00000255046	Chromatin interaction
ENSG00000231345	Chromatin interaction
ENSG00000171161	Chromatin interaction
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12241969	1.00[EUR][1000 genomes]
rs12267258	1.00[EUR][1000 genomes]
rs12571898	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12572578	1.00[EUR][1000 genomes]
rs16906575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16907261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4615973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55703887	1.00[EUR][1000 genomes]
rs55928478	1.00[EUR][1000 genomes]
rs56039956	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57040666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57073115	1.00[EUR][1000 genomes]
rs57238750	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57253864	1.00[EUR][1000 genomes]
rs57574235	1.00[EUR][1000 genomes]
rs57871603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60613759	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60974974	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61027189	1.00[EUR][1000 genomes]
rs61518314	1.00[EUR][1000 genomes]
rs61615406	1.00[EUR][1000 genomes]
rs7080895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7083978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7093159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73318780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73320893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73320899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7908759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52380800-52385400	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:52381200-52386000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:52381400-52385400	Active TSS	Brain Cingulate Gyrus	brain
4	chr10:52381400-52385800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:52381400-52386000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:52381400-52386200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr10:52381600-52385200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:52381600-52385200	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr10:52381600-52385200	Active TSS	Brain Hippocampus Middle	brain
10	chr10:52381600-52385400	Active TSS	Psoas Muscle	Psoas
11	chr10:52381600-52385600	Active TSS	Colon Smooth Muscle	Colon
12	chr10:52381600-52385600	Active TSS	Left Ventricle	heart
13	chr10:52381600-52385600	Active TSS	Ovary	ovary
14	chr10:52381600-52385800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr10:52381600-52385800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr10:52381600-52385800	Active TSS	Fetal Heart	heart
17	chr10:52381800-52385200	Active TSS	Primary T cells from cord blood	blood
18	chr10:52381800-52385400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:52381800-52385400	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr10:52381800-52385400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr10:52381800-52385400	Active TSS	Brain Angular Gyrus	brain
22	chr10:52381800-52385400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr10:52381800-52385400	Active TSS	Brain Substantia Nigra	brain
24	chr10:52381800-52385400	Active TSS	Fetal Intestine Small	intestine
25	chr10:52381800-52385400	Active TSS	Fetal Kidney	kidney
26	chr10:52381800-52385400	Active TSS	Lung	lung
27	chr10:52381800-52385400	Active TSS	Small Intestine	intestine
28	chr10:52381800-52385400	Active TSS	Spleen	Spleen
29	chr10:52381800-52385400	Active TSS	GM12878-XiMat	blood
30	chr10:52381800-52385400	Active TSS	HSMMtube	muscle
31	chr10:52381800-52385600	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr10:52381800-52385600	Active TSS	Gastric	stomach
33	chr10:52381800-52385600	Active TSS	Pancreas	Pancrea
34	chr10:52381800-52385600	Active TSS	Right Ventricle	heart
35	chr10:52381800-52385600	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr10:52381800-52385800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:52381800-52385800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:52381800-52385800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr10:52381800-52385800	Active TSS	A549	lung
40	chr10:52381800-52386000	Active TSS	Fetal Intestine Large	intestine
41	chr10:52382000-52385200	Active TSS	Liver	Liver
42	chr10:52382000-52385200	Active TSS	Brain Anterior Caudate	brain
43	chr10:52382000-52385200	Active TSS	Thymus	Thymus
44	chr10:52382000-52385600	Active TSS	Aorta	Aorta
45	chr10:52382000-52385800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr10:52382200-52385200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr10:52382200-52385200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr10:52382200-52385200	Active TSS	Fetal Stomach	stomach
49	chr10:52382200-52385400	Active TSS	Fetal Lung	lung
50	chr10:52382200-52385400	Active TSS	Placenta Amnion	Placenta Amnion

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