Variant report

Variant	rs10493196
Chromosome Location	chr1:56046405-56046406
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	REST	chr1:56045967-56046895	H1-neurons	neurons:	n/a	chr1:56046353-56046361
2	JUND	chr1:56046225-56047124	SK-N-SH	brain:	n/a	chr1:56046781-56046792
3	EP300	chr1:56046342-56047225	SK-N-SH	brain:	n/a	n/a
4	EP300	chr1:56046330-56047202	SK-N-SH	brain:	n/a	n/a
5	NR3C1	chr1:56046380-56046891	A549	lung:	n/a	chr1:56046558-56046567 chr1:56046662-56046688 chr1:56046667-56046683
6	RCOR1	chr1:56045729-56047241	IMR90	lung:	n/a	n/a
7	NR3C1	chr1:56046351-56046990	A549	lung:	n/a	chr1:56046558-56046567 chr1:56046662-56046688 chr1:56046667-56046683
8	EP300	chr1:56046313-56047134	SK-N-SH	brain:	n/a	n/a
9	TCF7L2	chr1:56046071-56046975	HCT-116	colon:	n/a	n/a
10	SP1	chr1:56046339-56047124	HCT-116	colon:	n/a	n/a
11	REST	chr1:56046062-56046649	H1-neurons	neurons:	n/a	chr1:56046353-56046361
12	GATA3	chr1:56046401-56047090	SK-N-SH	brain:	n/a	n/a
13	CEBPB	chr1:56046391-56046993	IMR90	lung:	n/a	n/a
14	GATA3	chr1:56046351-56047246	SK-N-SH	brain:	n/a	n/a
15	PBX3	chr1:56046296-56047088	SK-N-SH	brain:	n/a	n/a
16	JUND	chr1:56046330-56047111	SK-N-SH	brain:	n/a	chr1:56046781-56046792
17	TCF12	chr1:56046273-56047248	SK-N-SH	brain:	n/a	n/a
18	NFIC	chr1:56046401-56047211	SK-N-SH	brain:	n/a	n/a
19	EP300	chr1:56046353-56047078	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000234810	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10789002	0.85[EUR][1000 genomes]
rs10789003	0.85[EUR][1000 genomes]
rs10789004	0.85[EUR][1000 genomes]
rs10888933	0.83[EUR][1000 genomes]
rs10888934	0.85[EUR][1000 genomes]
rs11206620	0.85[EUR][1000 genomes]
rs11206622	0.85[EUR][1000 genomes]
rs11206625	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11206629	0.85[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11206636	0.82[AMR][1000 genomes]
rs11206637	0.82[AMR][1000 genomes]
rs11206638	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11807964	0.84[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12026971	0.86[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12040862	0.84[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12041985	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs12071564	0.88[LWK][hapmap];0.83[YRI][hapmap]
rs12086546	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12088041	0.83[YRI][hapmap]
rs12128337	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12132336	0.82[AMR][1000 genomes]
rs12139752	0.82[AMR][1000 genomes]
rs12142554	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12401977	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1392128	0.85[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1392129	0.85[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1392130	0.82[AMR][1000 genomes]
rs1587432	0.82[AMR][1000 genomes]
rs1604016	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17112402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17112410	0.91[YRI][hapmap]
rs17112413	0.90[YRI][hapmap]
rs17417716	0.85[EUR][1000 genomes]
rs4339898	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56169646	0.85[EUR][1000 genomes]
rs61774741	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61776360	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61776375	0.85[EUR][1000 genomes]
rs61776377	0.85[EUR][1000 genomes]
rs6588566	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6669248	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675850	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6677373	0.83[YRI][hapmap]
rs7513395	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7520444	0.91[YRI][hapmap]
rs7544458	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7546899	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7555929	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7556008	0.82[AMR][1000 genomes]
rs904602	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs9787362	0.82[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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10493196	GLIS1	cis	parietal	SCAN
rs10493196	BRP44	trans	cerebellum	SCAN
rs10493196	KTI12	cis	cerebellum	SCAN
rs10493196	C1orf168	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56037200-56047200	Weak transcription	Esophagus	oesophagus
2	chr1:56039000-56046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:56039200-56047200	Weak transcription	Psoas Muscle	Psoas
4	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:56042000-56046600	Weak transcription	Brain Anterior Caudate	brain
6	chr1:56042000-56047400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:56042200-56046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:56042200-56046600	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:56042200-56049600	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:56042200-56052400	Weak transcription	Right Atrium	heart
11	chr1:56043000-56049600	Weak transcription	Brain Germinal Matrix	brain
12	chr1:56043000-56049800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:56043000-56050200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:56043000-56050400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:56044400-56051400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:56044600-56048400	Enhancers	HSMM	muscle
17	chr1:56044800-56046800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:56045000-56047600	Enhancers	Osteobl	bone
19	chr1:56045000-56048200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:56045000-56048400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:56045200-56048200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:56045200-56048400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:56045200-56050000	Weak transcription	Ovary	ovary
24	chr1:56045400-56046600	Weak transcription	Fetal Lung	lung
25	chr1:56045400-56047200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:56045400-56048600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:56045600-56049600	Weak transcription	Fetal Stomach	stomach
28	chr1:56045800-56048400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:56046000-56048000	Enhancers	NHEK	skin
30	chr1:56046000-56048200	Enhancers	NHLF	lung
31	chr1:56046000-56048400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:56046200-56046600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:56046200-56047000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:56046200-56047000	Enhancers	Brain Substantia Nigra	brain
35	chr1:56046200-56047000	Enhancers	Rectal Smooth Muscle	rectum
36	chr1:56046200-56047400	Enhancers	NH-A	brain
37	chr1:56046400-56046600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:56046400-56046600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:56046400-56046600	Enhancers	Aorta	Aorta
40	chr1:56046400-56046600	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr1:56046400-56046600	Flanking Active TSS	HMEC	breast
42	chr1:56046400-56046600	Flanking Active TSS	NHDF-Ad	bronchial
43	chr1:56046400-56046800	Active TSS	HSMMtube	muscle
44	chr1:56046400-56047000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:56046400-56047000	Enhancers	Brain Angular Gyrus	brain
46	chr1:56046400-56047000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:56046400-56047000	Enhancers	Colon Smooth Muscle	Colon
48	chr1:56046400-56047000	Enhancers	A549	lung
49	chr1:56046400-56048000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr1:56046400-56048200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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