Variant report

Variant	rs3758402
Chromosome Location	chr10:45475917-45475918
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	BHLHE40	chr10:45475771-45476109	GM12878	blood:	n/a	n/a
2	MYBL2	chr10:45475803-45477077	HepG2	liver:	n/a	n/a
3	JUND	chr10:45475822-45476507	HepG2	liver:	n/a	chr10:45475955-45475963 chr10:45475956-45475963 chr10:45475955-45475963
4	EBF1	chr10:45475682-45476103	GM12878	blood:	n/a	n/a
5	RAD21	chr10:45475899-45476952	HepG2	liver:	n/a	chr10:45475916-45475926 chr10:45476201-45476213
6	RUNX3	chr10:45475595-45476227	GM12878	blood:	n/a	n/a
7	MTA3	chr10:45475774-45476298	GM12878	blood:	n/a	n/a
8	CHD2	chr10:45475712-45476197	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:45475700-45476350	GM12892	blood:	n/a	n/a
10	NFIC	chr10:45475663-45476979	GM12878	blood:	n/a	n/a
11	CHD1	chr10:45475869-45476198	GM12878	blood:	n/a	n/a
12	FOSL2	chr10:45475747-45476574	HepG2	liver:	n/a	chr10:45475955-45475963 chr10:45475956-45475963 chr10:45475955-45475963
13	MXI1	chr10:45475860-45476847	HepG2	liver:	n/a	n/a
14	EBF1	chr10:45475773-45476011	GM12878	blood:	n/a	n/a
15	POLR2A	chr10:45475620-45476218	GM12892	blood:	n/a	n/a
16	MAZ	chr10:45475722-45476107	GM12878	blood:	n/a	chr10:45475954-45475963
17	BCL3	chr10:45475655-45476179	GM12878	blood:	n/a	chr10:45475857-45475866
18	RCOR1	chr10:45475837-45476806	HepG2	liver:	n/a	n/a
19	NR2F2	chr10:45475763-45476750	HepG2	liver:	n/a	n/a
20	TCF3	chr10:45475909-45476058	GM12878	blood:	n/a	chr10:45476029-45476039
21	NFATC1	chr10:45475622-45476019	GM12878	blood:	n/a	n/a
22	EP300	chr10:45475706-45476716	HepG2	liver:	n/a	chr10:45476409-45476423
23	MBD4	chr10:45475756-45476668	HepG2	liver:	n/a	n/a
24	POLR2A	chr10:45475326-45477898	HepG2	liver:	n/a	n/a
25	STAT3	chr10:45475748-45475988	MCF10A-Er-Src	breast:	n/a	n/a
26	CHD2	chr10:45475754-45476424	HepG2	liver:	n/a	n/a
27	POLR2A	chr10:45475831-45476049	GM12878	blood:	n/a	n/a
28	POLR2A	chr10:45475830-45476204	HepG2	liver:	n/a	n/a
29	TCF12	chr10:45475789-45476003	GM12878	blood:	n/a	n/a
30	E2F6	chr10:45475411-45475973	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr10:45475836-45476399	HepG2	liver:	n/a	n/a
32	FOXA1	chr10:45475777-45476750	HepG2	liver:	n/a	n/a
33	SP1	chr10:45475748-45476058	GM12878	blood:	n/a	chr10:45475824-45475838
34	MXI1	chr10:45475760-45476046	GM12878	blood:	n/a	n/a
35	POLR2A	chr10:45475820-45477448	HepG2	liver:	n/a	n/a
36	WRNIP1	chr10:45475913-45476060	GM12878	blood:	n/a	n/a
37	FOS	chr10:45475793-45476004	MCF10A-Er-Src	breast:	n/a	chr10:45475955-45475963 chr10:45475956-45475963 chr10:45475955-45475963
38	MAX	chr10:45475752-45476914	HepG2	liver:	n/a	chr10:45475954-45475963
39	EGR1	chr10:45475785-45476015	GM12878	blood:	n/a	chr10:45475885-45475899 chr10:45475900-45475914
40	MAZ	chr10:45475782-45478019	IMR90	lung:	n/a	chr10:45475954-45475963
41	STAT1	chr10:45475829-45475978	GM12878	blood:	n/a	n/a
42	MAX	chr10:45475572-45476056	GM12878	blood:	n/a	chr10:45475704-45475713 chr10:45475954-45475963
43	MAZ	chr10:45475852-45476901	HepG2	liver:	n/a	chr10:45475954-45475963
44	PML	chr10:45475520-45476244	GM12878	blood:	n/a	n/a
45	RUNX3	chr10:45475664-45476181	GM12878	blood:	n/a	n/a
46	POLR2A	chr10:45475837-45476136	GM12878	blood:	n/a	n/a
47	ZNF143	chr10:45475807-45476023	GM12878	blood:	n/a	n/a
48	MTA3	chr10:45475460-45477050	GM12878	blood:	n/a	n/a
49	HEY1	chr10:45475907-45476491	HepG2	liver:	n/a	n/a
50	ELF1	chr10:45475774-45476302	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:45472874..45476114-chr10:45485945..45489321,3	MCF-7	breast:
2	chr10:45472768..45475523-chr10:45475664..45479867,4	MCF-7	breast:
3	chr10:45473658..45475931-chr10:46089040..46091906,2	K562	blood:
4	chr10:45472274..45474352-chr10:45475240..45477414,3	K562	blood:

Variant related genes	Relation type
C10orf10	TF binding region
RASSF4	TF binding region
ENSG00000165406	Chromatin interaction
ENSG00000165507	Chromatin interaction
ENSG00000107551	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11239301	0.88[YRI][hapmap]
rs11818623	0.80[EUR][1000 genomes]
rs3740098	0.88[TSI][hapmap]
rs3758401	0.91[CEU][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4245615	0.86[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs7079700	0.84[YRI][hapmap]
rs869156	0.82[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs883733	0.87[EUR][1000 genomes]
rs883734	0.85[CEU][hapmap]
rs883735	0.88[TSI][hapmap]
rs914700	0.85[TSI][hapmap]

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	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3758402	C10orf10	cis	lymphoblastoid	seeQTL
rs3758402	GDF2	cis	cerebellum	SCAN
rs3758402	HNRNPF	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45470800-45476400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:45470800-45477800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr10:45470800-45479400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:45471400-45476600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr10:45471600-45476800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr10:45473000-45477800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr10:45473600-45476400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr10:45473600-45476800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:45473800-45476200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr10:45473800-45476200	Enhancers	Fetal Brain Male	brain
11	chr10:45474000-45476200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:45474000-45476200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:45474200-45476000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:45474200-45476400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:45474200-45476400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:45474200-45476600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr10:45474200-45476800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:45474200-45476800	Enhancers	Fetal Thymus	thymus
19	chr10:45474200-45477000	Enhancers	Brain Substantia Nigra	brain
20	chr10:45474200-45477200	Enhancers	Fetal Lung	lung
21	chr10:45474200-45477400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:45474200-45478200	Enhancers	Esophagus	oesophagus
23	chr10:45474200-45478200	Enhancers	Psoas Muscle	Psoas
24	chr10:45474200-45478400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr10:45474200-45478800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:45474200-45479000	Enhancers	Stomach Mucosa	stomach
27	chr10:45474200-45479000	Enhancers	HUVEC	blood vessel
28	chr10:45474400-45476000	Enhancers	HSMMtube	muscle
29	chr10:45474400-45476000	Enhancers	NH-A	brain
30	chr10:45474400-45476200	Enhancers	Lung	lung
31	chr10:45474400-45476400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr10:45474400-45476400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:45474400-45476400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr10:45474400-45476400	Enhancers	Brain Germinal Matrix	brain
35	chr10:45474400-45476600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr10:45474400-45476600	Enhancers	Aorta	Aorta
37	chr10:45474400-45476600	Enhancers	Brain Hippocampus Middle	brain
38	chr10:45474400-45476600	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr10:45474400-45476800	Enhancers	NHDF-Ad	bronchial
40	chr10:45474400-45477200	Enhancers	Primary hematopoietic stem cells	blood
41	chr10:45474400-45477400	Enhancers	Brain Angular Gyrus	brain
42	chr10:45474400-45477400	Enhancers	Pancreas	Pancrea
43	chr10:45474400-45477400	Flanking Active TSS	HepG2	liver
44	chr10:45474400-45477600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr10:45474400-45477600	Enhancers	GM12878-XiMat	blood
46	chr10:45474400-45478000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr10:45474400-45478200	Enhancers	Fetal Stomach	stomach
48	chr10:45474400-45478400	Enhancers	Right Atrium	heart
49	chr10:45474400-45478600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr10:45474400-45478800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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