Variant report

Variant	rs1635553
Chromosome Location	chr12:48375568-48375569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:48375316-48375824	K562	blood:	n/a	n/a
2	E2F6	chr12:48375566-48375687	K562	blood:	n/a	n/a
3	BHLHE40	chr12:48375432-48375854	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48375228..48376777-chr12:48381596..48383195,2	MCF-7	breast:
2	chr12:48373823..48376376-chr12:48383731..48387007,3	MCF-7	breast:
3	chr12:48370423..48373200-chr12:48373445..48376245,2	K562	blood:
4	chr12:48262428..48264401-chr12:48374730..48377595,2	K562	blood:
5	chr12:48372717..48377052-chr12:48391617..48394178,3	MCF-7	breast:

No data

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11168337	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12721428	0.85[JPT][hapmap]
rs1621710	0.83[EUR][1000 genomes]
rs1635537	0.83[EUR][1000 genomes]
rs1635544	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1635546	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1635547	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1635550	0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1793911	0.82[EUR][1000 genomes]
rs1793923	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1793924	0.82[EUR][1000 genomes]
rs1793937	0.80[AMR][1000 genomes]
rs2070739	0.85[JPT][hapmap]
rs2276454	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2276455	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2276456	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2276457	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3829736	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740024	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv525456	chr12:48366449-48376969	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv558789	chr12:48368541-48376869	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1635553	ASB8	cis	cerebellum	SCAN
rs1635553	PRKAG1	cis	parietal	SCAN
rs1635553	LMBR1L	cis	cerebellum	SCAN
rs1635553	DBX2	cis	cerebellum	SCAN
rs1635553	PRPF40B	cis	parietal	SCAN
rs1635553	FAM186B	cis	cerebellum	SCAN
rs1635553	PRICKLE1	cis	parietal	SCAN
rs1635553	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1635553	LOC255411	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
4	chr12:48364400-48381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48365200-48381600	Weak transcription	Right Atrium	heart
6	chr12:48365400-48381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:48366200-48381200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:48366200-48381400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48366200-48381600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48372400-48378400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:48373800-48376800	Enhancers	Fetal Intestine Large	intestine
12	chr12:48374200-48377600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:48374400-48376400	Genic enhancers	Fetal Intestine Small	intestine
14	chr12:48374800-48375600	Enhancers	Duodenum Mucosa	Duodenum
15	chr12:48374800-48375600	Bivalent Enhancer	Stomach Mucosa	stomach
16	chr12:48374800-48375800	Enhancers	Colonic Mucosa	Colon
17	chr12:48374800-48375800	Enhancers	Fetal Heart	heart
18	chr12:48374800-48375800	Enhancers	Fetal Lung	lung
19	chr12:48374800-48375800	Flanking Active TSS	HepG2	liver
20	chr12:48374800-48379000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:48375000-48375600	Bivalent Enhancer	Fetal Stomach	stomach
22	chr12:48375000-48375600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr12:48375000-48375600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:48375000-48376000	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr12:48375000-48381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:48375200-48375600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:48375200-48375600	Enhancers	Lung	lung
28	chr12:48375200-48375600	Enhancers	K562	blood
29	chr12:48375200-48375800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr12:48375200-48381200	Weak transcription	Fetal Muscle Leg	muscle

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