Variant report

Variant	rs6735296
Chromosome Location	chr2:58468760-58468761
allele	A/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	POLR2A	chr2:58467996-58468848	GM19099	blood:	n/a	n/a
2	BCLAF1	chr2:58468029-58468813	GM12878	blood:	n/a	chr2:58468232-58468241 chr2:58468295-58468308
3	ZBTB33	chr2:58468258-58468781	A549	lung:	n/a	n/a
4	RFX5	chr2:58468017-58468859	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:58467566-58468913	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:58467943-58468811	GM18526	blood:	n/a	n/a
7	MAX	chr2:58467698-58468881	NB4	blood:	n/a	n/a
8	ELF1	chr2:58468200-58468793	A549	lung:	n/a	n/a
9	RFX5	chr2:58468443-58468882	K562	blood:	n/a	n/a
10	ELK1	chr2:58468442-58468969	K562	blood:	n/a	n/a
11	POLR2A	chr2:58468017-58468792	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr2:58467950-58468805	GM12892	blood:	n/a	n/a
13	TEAD4	chr2:58468331-58468779	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr2:58467696-58468767	K562	blood:	n/a	n/a
15	GABPA	chr2:58468015-58468932	A549	lung:	n/a	chr2:58468497-58468511 chr2:58468135-58468144 chr2:58468499-58468508 chr2:58468497-58468508
16	ZNF217	chr2:58468472-58468768	MCF-7	breast:	n/a	n/a
17	SETDB1	chr2:58468098-58468810	K562	blood:	n/a	n/a
18	SMC3	chr2:58468261-58468799	HepG2	liver:	n/a	n/a
19	MXI1	chr2:58467660-58468786	HepG2	liver:	n/a	n/a
20	MAX	chr2:58467767-58468986	A549	lung:	n/a	n/a
21	POLR2A	chr2:58467917-58468866	GM12892	blood:	n/a	n/a
22	MAZ	chr2:58468017-58468843	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr2:58467965-58468821	GM19193	blood:	n/a	n/a
24	POLR2A	chr2:58467756-58468782	U87	brain:	n/a	n/a
25	ELF1	chr2:58468287-58468781	K562	blood:	n/a	n/a
26	POLR2A	chr2:58468046-58468784	GM12891	blood:	n/a	n/a
27	BHLHE40	chr2:58468368-58468790	K562	blood:	n/a	n/a
28	MAX	chr2:58467861-58468871	ECC-1	luminal epithelium:	n/a	n/a
29	SMARCB1	chr2:58467944-58468819	Hela-S3	cervix:	n/a	n/a
30	NFIC	chr2:58467485-58468912	HepG2	liver:	n/a	chr2:58467886-58467903 chr2:58467885-58467901 chr2:58467885-58467902 chr2:58467887-58467903
31	MAZ	chr2:58467881-58469083	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:58467903-58468822	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:58467771-58468830	K562	blood:	n/a	n/a
34	POLR2A	chr2:58468080-58468776	GM12878	blood:	n/a	n/a
35	SP1	chr2:58468078-58468824	A549	lung:	n/a	chr2:58468109-58468119
36	MAX	chr2:58467888-58468850	K562	blood:	n/a	n/a
37	ZNF143	chr2:58468278-58468810	K562	blood:	n/a	n/a
38	POLR2A	chr2:58468083-58468831	GM12892	blood:	n/a	n/a
39	E2F4	chr2:58468206-58468895	Hela-S3	cervix:	n/a	chr2:58468550-58468561 chr2:58468498-58468507 chr2:58468549-58468561
40	TAF1	chr2:58468067-58468801	K562	blood:	n/a	n/a
41	E2F1	chr2:58468019-58468821	Hela-S3	cervix:	n/a	chr2:58468498-58468507 chr2:58468549-58468560 chr2:58468549-58468561
42	POLR2A	chr2:58468017-58468823	MCF-7	breast:	n/a	n/a
43	GABPA	chr2:58468229-58468903	SK-N-SH	brain:	n/a	chr2:58468497-58468511 chr2:58468499-58468508 chr2:58468497-58468508
44	POLR2A	chr2:58467749-58468782	U87	brain:	n/a	n/a
45	ZKSCAN1	chr2:58468310-58468818	Hela-S3	cervix:	n/a	n/a
46	ELF1	chr2:58468288-58468840	A549	lung:	n/a	n/a
47	POLR2A	chr2:58467444-58468816	K562	blood:	n/a	n/a
48	HEY1	chr2:58467916-58468835	HepG2	liver:	n/a	chr2:58468183-58468198
49	CTCF	chr2:58468660-58468810	BJ	skin:	n/a	n/a
50	RELA	chr2:58467774-58468828	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:58468655..58470586-chr2:58617618..58620030,2	K562	blood:
2	chr2:58468236..58468953-chr5:34007718..34008263,2	HCT-116	colon:
3	chr2:58454709..58457250-chr2:58468268..58470995,2	K562	blood:
4	chr2:58468542..58470119-chr2:58479587..58481216,2	K562	blood:
5	chr2:58272245..58275889-chr2:58464232..58469335,5	K562	blood:
6	chr2:58468241..58469136-chr2:96874014..96874530,2	Hela-S3	cervix:
7	chr2:58455073..58459456-chr2:58466641..58469255,4	K562	blood:
8	chr12:120729524..120730072-chr2:58468187..58468827,2	NB4	blood:
9	chr19:40476701..40477573-chr2:58468129..58468983,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VRK2-9	chr2:58468484-58468821	ENSG00000273063.1

Variant related genes	Relation type
FANCL	TF binding region
ENSG00000204685	Chromatin interaction
ENSG00000115392	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000242110	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11125742	0.93[CEU][hapmap];1.00[TSI][hapmap]
rs11125745	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11889211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12469873	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475594	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13422644	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17049378	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs17049429	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2192690	0.94[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771215	0.93[CEU][hapmap]
rs3771220	0.82[YRI][hapmap]
rs4395240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56705143	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56730649	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6713551	0.86[CEU][hapmap];0.93[TSI][hapmap]
rs6725148	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6732505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72810360	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72810373	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72812357	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594702	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6735296	PUS10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58465800-58468800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:58466200-58468800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:58466600-58468800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:58466600-58469000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:58467000-58469000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:58467400-58468800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:58467400-58468800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:58467400-58468800	Active TSS	Colonic Mucosa	Colon
9	chr2:58467400-58468800	Active TSS	Fetal Intestine Small	intestine
10	chr2:58467400-58468800	Active TSS	Pancreas	Pancrea
11	chr2:58467400-58468800	Active TSS	HSMM	muscle
12	chr2:58467400-58469000	Active TSS	Fetal Kidney	kidney
13	chr2:58467400-58469000	Active TSS	Right Atrium	heart
14	chr2:58467600-58468800	Active TSS	Left Ventricle	heart
15	chr2:58467600-58468800	Active TSS	Placenta Amnion	Placenta Amnion
16	chr2:58467600-58468800	Active TSS	Right Ventricle	heart
17	chr2:58467600-58468800	Active TSS	NHLF	lung
18	chr2:58467600-58469000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr2:58467600-58469000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:58467600-58469000	Active TSS	Brain Anterior Caudate	brain
21	chr2:58467600-58469000	Active TSS	Brain Germinal Matrix	brain
22	chr2:58467600-58469000	Active TSS	Fetal Muscle Leg	muscle
23	chr2:58467600-58469000	Active TSS	Fetal Thymus	thymus
24	chr2:58467600-58469000	Active TSS	Ovary	ovary
25	chr2:58467600-58469000	Active TSS	Thymus	Thymus
26	chr2:58467800-58468800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr2:58467800-58468800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:58467800-58468800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:58467800-58468800	Active TSS	Aorta	Aorta
30	chr2:58467800-58468800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:58467800-58468800	Active TSS	Brain Substantia Nigra	brain
32	chr2:58467800-58468800	Active TSS	Colon Smooth Muscle	Colon
33	chr2:58467800-58468800	Active TSS	Esophagus	oesophagus
34	chr2:58467800-58468800	Active TSS	Fetal Intestine Large	intestine
35	chr2:58467800-58468800	Active TSS	Lung	lung
36	chr2:58467800-58468800	Active TSS	A549	lung
37	chr2:58467800-58468800	Active TSS	NHDF-Ad	bronchial
38	chr2:58467800-58469000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:58467800-58469000	Active TSS	Primary T cells fromperipheralblood	blood
40	chr2:58467800-58469000	Active TSS	Brain Angular Gyrus	brain
41	chr2:58467800-58469000	Active TSS	Brain Cingulate Gyrus	brain
42	chr2:58467800-58469000	Active TSS	Fetal Stomach	stomach
43	chr2:58467800-58469000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr2:58467800-58469000	Active TSS	Rectal Smooth Muscle	rectum
45	chr2:58467800-58469000	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr2:58467800-58469200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr2:58468000-58468800	Active TSS	Primary B cells from cord blood	blood
48	chr2:58468000-58468800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:58468000-58468800	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr2:58468000-58468800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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