Variant report

Variant	rs17374902
Chromosome Location	chr4:95128677-95128678
allele	C/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	ATF2	chr4:95128494-95129294	GM12878	blood:	n/a	n/a
2	MAX	chr4:95128632-95129397	HepG2	liver:	n/a	chr4:95129125-95129135 chr4:95129327-95129337 chr4:95129270-95129280
3	MAX	chr4:95128569-95129443	H1-hESC	embryonic stem cell:	n/a	chr4:95129125-95129135 chr4:95129327-95129337 chr4:95129270-95129280
4	YY1	chr4:95128586-95129226	GM12892	blood:	n/a	n/a
5	CEBPB	chr4:95128562-95129270	H1-hESC	embryonic stem cell:	n/a	chr4:95128749-95128760
6	MYC	chr4:95128559-95129614	K562	blood:	n/a	chr4:95129125-95129135 chr4:95129327-95129337 chr4:95129270-95129280
7	GATA1	chr4:95128574-95129572	PBDE	blood:	n/a	n/a
8	ATF3	chr4:95128597-95129058	K562	blood:	n/a	n/a
9	GTF2F1	chr4:95128599-95129277	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOSL2	chr4:95128587-95129222	HepG2	liver:	n/a	n/a
11	MTA3	chr4:95128603-95129100	GM12878	blood:	n/a	n/a
12	SMC3	chr4:95128635-95129269	Hela-S3	cervix:	n/a	chr4:95129128-95129138
13	CBX3	chr4:95128395-95129349	HCT-116	colon:	n/a	n/a
14	TCF7L2	chr4:95128672-95129024	PANC-1	pancreas:	n/a	n/a
15	MXI1	chr4:95128533-95129393	Hela-S3	cervix:	n/a	n/a
16	ELF1	chr4:95128539-95129358	GM12878	blood:	n/a	chr4:95129022-95129031
17	EP300	chr4:95128544-95129451	ECC-1	luminal epithelium:	n/a	chr4:95129022-95129029
18	MAFF	chr4:95128556-95128970	K562	blood:	n/a	chr4:95128750-95128768
19	CEBPB	chr4:95128569-95129054	MCF-7	breast:	n/a	chr4:95128749-95128760
20	ELF1	chr4:95128657-95129177	A549	lung:	n/a	chr4:95129022-95129031
21	NFIC	chr4:95128532-95129318	HepG2	liver:	n/a	chr4:95129024-95129052
22	MYC	chr4:95128559-95129767	A549	lung:	n/a	chr4:95129125-95129135 chr4:95129327-95129337 chr4:95129270-95129280
23	POLR2A	chr4:95128560-95129377	K562	blood:	n/a	n/a
24	POLR2A	chr4:95128577-95129460	MCF-7	breast:	n/a	n/a
25	SIN3A	chr4:95128604-95129501	GM12878	blood:	n/a	chr4:95129098-95129111
26	ZBTB33	chr4:95128558-95129144	A549	lung:	n/a	n/a
27	POLR2A	chr4:95128507-95129609	GM18505	blood:	n/a	n/a
28	ETS1	chr4:95128599-95129254	GM12878	blood:	n/a	chr4:95129021-95129030 chr4:95129019-95129030 chr4:95129019-95129029
29	CEBPB	chr4:95128486-95129371	A549	lung:	n/a	chr4:95128749-95128760
30	CHD2	chr4:95128486-95129273	Hela-S3	cervix:	n/a	chr4:95128710-95128720
31	TAF1	chr4:95128640-95129327	GM12878	blood:	n/a	n/a
32	YY1	chr4:95128588-95129298	ECC-1	luminal epithelium:	n/a	chr4:95129267-95129278 chr4:95129270-95129284
33	PML	chr4:95128516-95129274	GM12878	blood:	n/a	n/a
34	GTF2B	chr4:95128670-95129347	K562	blood:	n/a	n/a
35	FOS	chr4:95128567-95129128	MCF10A-Er-Src	breast:	n/a	n/a
36	ELK1	chr4:95128560-95129251	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr4:95128673-95129350	HepG2	liver:	n/a	n/a
38	TAF1	chr4:95128501-95129432	K562	blood:	n/a	n/a
39	MTA3	chr4:95128506-95129639	GM12878	blood:	n/a	n/a
40	BRCA1	chr4:95128541-95129157	GM12878	blood:	n/a	n/a
41	TBL1XR1	chr4:95128589-95129242	K562	blood:	n/a	n/a
42	MYBL2	chr4:95128546-95129346	HepG2	liver:	n/a	n/a
43	USF2	chr4:95128628-95128877	Hela-S3	cervix:	n/a	n/a
44	KAP1	chr4:95128578-95129088	U2OS	brain:	n/a	n/a
45	ELF1	chr4:95128520-95129228	A549	lung:	n/a	chr4:95129022-95129031
46	POLR2A	chr4:95128586-95129303	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr4:95128602-95129267	A549	lung:	n/a	n/a
48	RCOR1	chr4:95128616-95129209	K562	blood:	n/a	n/a
49	CREB1	chr4:95128580-95129293	A549	lung:	n/a	n/a
50	ZBTB33	chr4:95128527-95129209	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:95128661-95128711	AG10803	skin:	n/a
2	chr4:95128661-95128711	Caco-2	colon:	n/a
3	chr4:95128661-95128711	IMR90	lung:	fetal
4	chr4:95128673-95128723	GM19239	blood:	n/a
5	chr4:95128661-95128711	HCM	heart:	n/a
6	chr4:95128667-95128717	NHBE	bronchial:	n/a
7	chr4:95128661-95128711	A549	lung:	n/a
8	chr4:95128667-95128717	PFSK-1	brain:	n/a
9	chr4:95128667-95128717	HUVEC	blood vessel:	n/a
10	chr4:95128667-95128717	BE2_C	brain:	n/a
11	chr4:95128673-95128723	SK-N-SH	brain:	n/a
12	chr4:95128667-95128717	HAEpiC	amniotic membrane:	n/a
13	chr4:95128667-95128717	A549	lung:	n/a
14	chr4:95128673-95128723	AG10803	skin:	n/a
15	chr4:95128667-95128717	HCPEpiC	choroid plexus:	n/a
16	chr4:95128661-95128711	SK-N-MC	brain:	n/a
17	chr4:95128673-95128723	HL-60	blood:	n/a
18	chr4:95128673-95128723	Hepatocyte	liver:	n/a
19	chr4:95128667-95128717	IMR90	lung:	fetal
20	chr4:95128667-95128717	PANC-1	pancreas:	n/a
21	chr4:95128667-95128717	HL-60	blood:	n/a
22	chr4:95128673-95128723	HCM	heart:	n/a
23	chr4:95128667-95128717	SK-N-SH_RA	brain:	n/a
24	chr4:95128667-95128717	Jurkat	blood:	n/a
25	chr4:95128667-95128717	AG09319	gingival:	n/a
26	chr4:95128661-95128711	ovcar-3	ovarian:	n/a
27	chr4:95128667-95128717	H1-hESC	embryonic stem cell:	embryo
28	chr4:95128673-95128723	SKMC	muscle:	n/a
29	chr4:95128667-95128717	HepG2	liver:	n/a
30	chr4:95128661-95128711	SK-N-SH	brain:	n/a
31	chr4:95128661-95128711	HNPCEpiC	eye:	n/a
32	chr4:95128661-95128711	PANC-1	pancreas:	n/a
33	chr4:95128673-95128723	SAEC	small airway:	n/a
34	chr4:95128673-95128723	A549	lung:	n/a
35	chr4:95128661-95128711	PrEC	prostate:	n/a
36	chr4:95128661-95128711	ProgFib	skin:	n/a
37	chr4:95128661-95128711	NT2-D1	testis:	n/a
38	chr4:95128673-95128723	MCF-7	breast:	n/a
39	chr4:95128673-95128723	T-47D	breast:	n/a
40	chr4:95128673-95128723	HIPEpiC	eye:	n/a
41	chr4:95128673-95128723	Caco-2	colon:	n/a
42	chr4:95128661-95128711	K562	blood:	n/a
43	chr4:95128667-95128717	GM12891	blood:	n/a
44	chr4:95128661-95128711	H1-hESC	embryonic stem cell:	embryo
45	chr4:95128673-95128723	IMR90	lung:	fetal
46	chr4:95128673-95128723	SK-N-SH_RA	brain:	n/a
47	chr4:95128661-95128711	AG09309	skin:	n/a
48	chr4:95128673-95128723	Hela-S3	cervix:	n/a
49	chr4:95128673-95128723	GM12892	blood:	n/a
50	chr4:95128667-95128717	GM12892	blood:	n/a

Variant related genes	Relation type
SMARCAD1	TF binding region
SMARCAD1	CpG island

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10003038	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10007463	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10011158	0.80[EUR][1000 genomes]
rs10013456	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10014718	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10016925	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10018599	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10022350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10022504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025333	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025839	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027578	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10029551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10030605	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10032125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10084984	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10516948	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11943524	0.81[AMR][1000 genomes]
rs12186176	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1509944	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17301787	1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs17303283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17310498	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17374964	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17376684	1.00[CEU][hapmap]
rs28379069	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28419190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28442028	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28463840	0.81[EUR][1000 genomes]
rs28470897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28544271	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28565382	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28568937	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28611432	0.80[EUR][1000 genomes]
rs28638427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28650373	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28676794	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28733161	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28795707	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56110205	0.80[EUR][1000 genomes]
rs6811367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813439	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6815436	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6817118	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6834248	0.82[CEU][hapmap];0.93[TSI][hapmap]
rs6844517	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6848288	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6857003	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs728989	0.82[CEU][hapmap]
rs7653910	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7654621	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660243	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7698171	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7699500	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9307138	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9307140	0.93[CEU][hapmap]
rs9884428	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9991214	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992255	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9999328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999656	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][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	nsv879618	chr4:94980768-95136164	Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95128000-95128800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
2	chr4:95128000-95129400	Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr4:95128000-95129400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:95128000-95129600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr4:95128000-95129600	Active TSS	Fetal Kidney	kidney
6	chr4:95128000-95129600	Active TSS	K562	blood
7	chr4:95128000-95129800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:95128000-95129800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:95128000-95129800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:95128000-95129800	Active TSS	Stomach Smooth Muscle	stomach
11	chr4:95128000-95129800	Active TSS	GM12878-XiMat	blood
12	chr4:95128000-95130000	Active TSS	Fetal Brain Male	brain
13	chr4:95128200-95128800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:95128200-95128800	Active TSS	Right Atrium	heart
15	chr4:95128200-95129200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr4:95128200-95129400	Active TSS	Primary T cells fromperipheralblood	blood
17	chr4:95128200-95129400	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr4:95128200-95129400	Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr4:95128200-95129400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:95128200-95129400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:95128200-95129400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr4:95128200-95129400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:95128200-95129400	Active TSS	Adipose Nuclei	Adipose
24	chr4:95128200-95129400	Active TSS	Brain Anterior Caudate	brain
25	chr4:95128200-95129400	Active TSS	Fetal Thymus	thymus
26	chr4:95128200-95129400	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr4:95128200-95129400	Active TSS	HUVEC	blood vessel
28	chr4:95128200-95129400	Active TSS	Monocytes-CD14+_RO01746	blood
29	chr4:95128200-95129600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:95128200-95129600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:95128200-95129600	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr4:95128200-95129600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:95128200-95129600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:95128200-95129600	Active TSS	Brain Angular Gyrus	brain
35	chr4:95128200-95129600	Active TSS	Brain Substantia Nigra	brain
36	chr4:95128200-95129600	Active TSS	Duodenum Mucosa	Duodenum
37	chr4:95128200-95129600	Active TSS	Fetal Intestine Large	intestine
38	chr4:95128200-95129600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr4:95128200-95129600	Active TSS	Fetal Lung	lung
40	chr4:95128200-95129600	Active TSS	Placenta	Placenta
41	chr4:95128200-95129600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:95128200-95129600	Active TSS	Rectal Smooth Muscle	rectum
43	chr4:95128200-95129600	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr4:95128200-95129600	Active TSS	Thymus	Thymus
45	chr4:95128200-95129600	Active TSS	NH-A	brain
46	chr4:95128200-95129600	Active TSS	NHEK	skin
47	chr4:95128200-95129600	Active TSS	Osteobl	bone
48	chr4:95128200-95129800	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr4:95128200-95129800	Active TSS	H1 Cell Line	embryonic stem cell
50	chr4:95128200-95129800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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