Variant report

Variant	rs4660818
Chromosome Location	chr1:45139252-45139253
allele	A/C
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	RFX5	chr1:45139067-45141154	SK-N-SH	brain:	n/a	chr1:45140267-45140281 chr1:45140214-45140223 chr1:45140269-45140278 chr1:45140266-45140281 chr1:45140212-45140226
2	STAT5A	chr1:45139236-45140256	GM12878	blood:	n/a	chr1:45139805-45139813
3	MTA3	chr1:45139205-45140785	GM12878	blood:	n/a	n/a
4	REST	chr1:45139044-45140898	H1-neurons	neurons:	n/a	chr1:45139733-45139746 chr1:45139735-45139744 chr1:45139524-45139542 chr1:45139729-45139749 chr1:45140710-45140720 chr1:45139730-45139748
5	MXI1	chr1:45138527-45141044	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45138566..45141370-chr1:45265919..45267652,2	K562	blood:
2	chr1:45138628..45142139-chr1:45284311..45287293,3	K562	blood:
3	chr1:45138846..45140419-chr1:45285413..45286988,2	K562	blood:
4	chr1:45138378..45140523-chr1:45195153..45198091,3	MCF-7	breast:
5	chr1:45095169..45100377-chr1:45133934..45142864,15	K562	blood:
6	chr1:45136867..45139801-chr1:45184892..45187716,2	MCF-7	breast:
7	chr1:45100701..45102574-chr1:45138081..45139709,2	K562	blood:
8	chr1:45102853..45104841-chr1:45137673..45140474,2	K562	blood:

Variant related genes	Relation type
C1orf228	TF binding region
ENSG00000200169	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000173846	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11581074	0.96[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582807	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588956	0.84[CHD][hapmap]
rs12022097	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1276066	0.88[AFR][1000 genomes]
rs1963490	0.95[ASN][1000 genomes]
rs2236219	0.81[CHD][hapmap]
rs34948326	0.96[ASN][1000 genomes]
rs3850853	0.96[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs3889696	0.93[EUR][1000 genomes]
rs4660821	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660822	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789885	0.91[EUR][1000 genomes]
rs6667593	0.83[YRI][hapmap]
rs6668870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678831	0.90[EUR][1000 genomes]
rs6683133	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs72899527	0.88[EUR][1000 genomes]
rs7538419	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs7539607	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4660818	SNORD38B	cis	cerebellum	SCAN
rs4660818	EIF2B3	cis	cerebellum	SCAN
rs4660818	MUTYH	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45136800-45139400	Enhancers	Primary B cells from peripheral blood	blood
2	chr1:45137000-45139400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:45137000-45139400	Enhancers	Spleen	Spleen
4	chr1:45137400-45139400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:45137400-45139800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:45137600-45139400	Enhancers	Lung	lung
7	chr1:45137600-45139600	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:45137600-45139800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:45137600-45139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:45137600-45139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:45137600-45139800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr1:45137800-45139400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:45137800-45139400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:45137800-45139400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:45137800-45139600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:45137800-45139600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr1:45138000-45139400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:45138000-45139600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:45138000-45139600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:45138200-45139400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:45138200-45139400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:45138400-45139400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:45138400-45139400	Enhancers	Esophagus	oesophagus
24	chr1:45138400-45139400	Enhancers	Pancreas	Pancrea
25	chr1:45138400-45139600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:45138400-45139600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr1:45138600-45139400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:45138600-45139400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:45138600-45139400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:45138600-45139400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:45138600-45139400	Enhancers	Aorta	Aorta
32	chr1:45138600-45139400	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr1:45138600-45139400	Flanking Active TSS	Colonic Mucosa	Colon
34	chr1:45138600-45139400	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr1:45138600-45139400	Enhancers	Gastric	stomach
36	chr1:45138600-45139400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:45138600-45139400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:45138600-45139600	Flanking Active TSS	Liver	Liver
39	chr1:45138600-45139600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr1:45138800-45139400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:45138800-45139400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:45138800-45139400	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr1:45138800-45139400	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr1:45138800-45139400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:45138800-45139400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:45138800-45139400	Flanking Active TSS	HepG2	liver
47	chr1:45138800-45139600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:45138800-45139600	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr1:45138800-45139600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:45138800-45139600	Flanking Active TSS	Fetal Intestine Large	intestine

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