Variant report

Variant	rs10516559
Chromosome Location	chr4:110746730-110746731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:110746462-110746946	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:110746563-110746952	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:110746307-110747138	K562	blood:	n/a	n/a
4	POLR2A	chr4:110746378-110746917	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110744505..110746809-chr4:110749659..110751838,2	K562	blood:
2	chr4:110736461..110738940-chr4:110744765..110747082,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CFI-2	chr4:110746298-110747043	NONHSAT097796

No data

Variant related genes	Relation type
RRH	TF binding region
ENSG00000109534	Chromatin interaction
ENSG00000272795	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10022841	0.88[CEU][hapmap]
rs12500239	0.83[EUR][1000 genomes]
rs12504835	0.83[EUR][1000 genomes]
rs12513108	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs12643147	0.83[EUR][1000 genomes]
rs12644142	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs13112387	0.83[EUR][1000 genomes]
rs13115969	0.83[CEU][hapmap]
rs13128244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[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];0.95[ASN][1000 genomes]
rs13140289	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs13141065	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs13150454	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs1860130	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2078040	0.83[CEU][hapmap]
rs2347130	0.83[CEU][hapmap]
rs34377477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34378309	0.83[EUR][1000 genomes]
rs34706258	0.81[EUR][1000 genomes]
rs35426158	0.83[EUR][1000 genomes]
rs3775961	0.83[CEU][hapmap]
rs4353905	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs4422417	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs4610335	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs4698749	0.88[CEU][hapmap]
rs4698750	0.83[EUR][1000 genomes]
rs4698751	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4698795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][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];0.95[ASN][1000 genomes]
rs4698799	0.81[AMR][1000 genomes]
rs55814498	0.81[AMR][1000 genomes]
rs62324955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62327573	0.87[EUR][1000 genomes]
rs6814743	0.88[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6816185	0.83[CEU][hapmap]
rs6841737	0.83[CEU][hapmap]
rs6842245	0.81[CEU][hapmap]
rs6858351	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs7657133	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs7678178	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs7698794	0.83[EUR][1000 genomes]

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	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10516559	ENPEP	cis	cerebellum	SCAN
rs10516559	RRH	cis	parietal	SCAN
rs10516559	FAM53B	trans	lymphoblastoid	seeQTL
rs10516559	RRH	cis	cerebellum	SCAN
rs10516559	CYP2U1	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110737600-110770600	Weak transcription	Aorta	Aorta
2	chr4:110737800-110748000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:110737800-110753200	Weak transcription	Lung	lung
4	chr4:110738000-110747200	Weak transcription	Gastric	stomach
5	chr4:110738000-110748400	Weak transcription	Small Intestine	intestine
6	chr4:110738000-110760800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:110738200-110747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:110738400-110748000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:110738400-110748000	Weak transcription	Ovary	ovary
10	chr4:110738400-110748400	Weak transcription	Right Ventricle	heart
11	chr4:110738400-110748600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:110738400-110757200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:110738600-110746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:110738600-110747000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:110738600-110747600	Weak transcription	Fetal Heart	heart
16	chr4:110738600-110748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:110738800-110746800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:110738800-110746800	Strong transcription	Adipose Nuclei	Adipose
19	chr4:110738800-110747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:110738800-110747000	Strong transcription	Fetal Thymus	thymus
21	chr4:110738800-110747000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr4:110738800-110747000	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr4:110738800-110747200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:110738800-110747200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:110738800-110747200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:110738800-110747600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:110738800-110748600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:110739000-110746800	Strong transcription	HUVEC	blood vessel
29	chr4:110739000-110747000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:110739000-110747000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr4:110739000-110747000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:110739000-110747000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:110739000-110747000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:110739000-110747000	Strong transcription	K562	blood
35	chr4:110739000-110747000	Strong transcription	Osteobl	bone
36	chr4:110739000-110748400	Weak transcription	Fetal Brain Male	brain
37	chr4:110739000-110749800	Weak transcription	NHLF	lung
38	chr4:110739200-110746800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:110739200-110747000	Strong transcription	Liver	Liver
40	chr4:110739200-110747200	Strong transcription	NH-A	brain
41	chr4:110739200-110748400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:110739200-110748600	Strong transcription	HSMM	muscle
43	chr4:110739400-110747000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr4:110739400-110747600	Strong transcription	Dnd41	blood
45	chr4:110739600-110746800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:110739800-110747000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr4:110739800-110747600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr4:110740000-110746800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr4:110740200-110746800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:110740400-110746800	Strong transcription	NHDF-Ad	bronchial

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