Variant report

Variant	rs10783779
Chromosome Location	chr12:56491880-56491881
allele	G/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	EGR1	chr12:56491642-56491881	K562	blood:	n/a	chr12:56491746-56491756 chr12:56491750-56491759 chr12:56491747-56491760
2	POLR2A	chr12:56491408-56492266	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56488978..56493403-chr12:56493768..56499691,12	MCF-7	breast:
2	chr12:56485510..56489387-chr12:56490839..56493900,6	K562	blood:
3	chr12:56486513..56489707-chr12:56489717..56492726,3	MCF-7	breast:

Variant related genes	Relation type
ERBB3	TF binding region
ENSG00000257411	TF binding region
ENSG00000257411	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000065361	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2271189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292238	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759094	0.86[ASN][1000 genomes]
rs705708	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Educational attainment	25201988	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10783779	SUOX	cis	cerebellum	SCAN
rs10783779	NCKAP1L	cis	cerebellum	SCAN
rs10783779	SMARCC2	cis	parietal	SCAN
rs10783779	RAB5B	cis	Muscle Skeletal	GTEx
rs10783779	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs10783779	ATP5G2	cis	parietal	SCAN
rs10783779	AC034102.1	cis	Muscle Skeletal	GTEx
rs10783779	ITGA7	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56474400-56497200	Weak transcription	Right Atrium	heart
2	chr12:56476200-56497200	Weak transcription	Fetal Kidney	kidney
3	chr12:56476600-56496400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:56476600-56497600	Weak transcription	Small Intestine	intestine
5	chr12:56477000-56497000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:56477000-56497000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:56477600-56496600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:56477800-56496200	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr12:56478600-56496400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:56479200-56496000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:56479200-56496400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:56479400-56496800	Strong transcription	Fetal Intestine Small	intestine
13	chr12:56479400-56497200	Strong transcription	Fetal Intestine Large	intestine
14	chr12:56480000-56495800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:56480000-56496400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:56480400-56493400	Weak transcription	NHEK	skin
17	chr12:56481200-56496200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:56481200-56496800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:56481200-56497000	Weak transcription	Hela-S3	cervix
20	chr12:56481400-56492400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:56481600-56496400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr12:56481600-56496600	Strong transcription	Placenta	Placenta
23	chr12:56481600-56497000	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:56481600-56497200	Strong transcription	Liver	Liver
25	chr12:56482800-56497600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:56484200-56496800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:56485000-56496000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:56485200-56496200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr12:56485200-56496400	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr12:56485800-56496200	Strong transcription	HepG2	liver
31	chr12:56486000-56496000	Strong transcription	Fetal Stomach	stomach
32	chr12:56486000-56496000	Strong transcription	Pancreas	Pancrea
33	chr12:56486400-56493000	Strong transcription	Esophagus	oesophagus
34	chr12:56486400-56495600	Strong transcription	Brain Substantia Nigra	brain
35	chr12:56486600-56494000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:56486600-56496000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:56486600-56496400	Strong transcription	Brain Hippocampus Middle	brain
38	chr12:56486800-56495600	Strong transcription	Gastric	stomach
39	chr12:56487000-56495000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:56487200-56495800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:56488400-56492400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:56488400-56497000	Weak transcription	Stomach Mucosa	stomach
43	chr12:56489200-56497600	Weak transcription	Lung	lung
44	chr12:56489800-56492600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr12:56489800-56496000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:56490000-56494000	Strong transcription	Colonic Mucosa	Colon
47	chr12:56490200-56495400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:56490600-56492400	Weak transcription	HSMMtube	muscle
49	chr12:56490600-56497400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:56491000-56494800	Weak transcription	Brain Anterior Caudate	brain

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