Variant report

Variant	rs3217753
Chromosome Location	chr4:122746325-122746326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZC3H11A	chr4:122746202-122746385	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:122745296..122747989-chr4:122762768..122765096,2	K562	blood:
2	chr4:122745115..122747989-chr4:122763596..122768679,4	K562	blood:
3	chr4:122719927..122724442-chr4:122741540..122746604,11	MCF-7	breast:
4	chr4:122613955..122616296-chr4:122745989..122748814,2	K562	blood:
5	chr4:122609696..122612214-chr4:122746290..122748516,2	K562	blood:
6	chr4:122743548..122747768-chr4:122748127..122751699,7	K562	blood:

No data

Variant related genes	Relation type
CCNA2	TF binding region
ENSG00000138686	Chromatin interaction
ENSG00000123737	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11098645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098648	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731570	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12502635	0.88[CHB][hapmap]
rs12512876	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12650359	0.88[CHB][hapmap]
rs1396080	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1507994	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507995	0.84[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452156	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071486	0.91[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2221628	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3217771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217780	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828485	0.82[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924987	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4077102	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516739	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56077950	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159666	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56311153	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58649165	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61217486	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534323	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67772833	0.95[EUR][1000 genomes]
rs6813653	0.81[ASN][1000 genomes]
rs6815790	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821305	0.90[ASN][1000 genomes]
rs6823818	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824258	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs6826506	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838153	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855269	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680779	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660548	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686200	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691955	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs769238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769246	0.92[EUR][1000 genomes]
rs7699776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684587	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3217753	BBS7	cis	parietal	SCAN
rs3217753	BBS7	cis	cerebellum	SCAN
rs3217753	EXOSC9	cis	lymphoblastoid	seeQTL
rs3217753	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122744600-122746400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:122745400-122748200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:122745400-122750600	Weak transcription	Gastric	stomach
4	chr4:122745400-122750600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:122745400-122751200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:122745400-122753200	Weak transcription	Lung	lung
7	chr4:122745400-122767200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:122745400-122777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:122745400-122790400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:122745400-122790600	Weak transcription	Small Intestine	intestine
11	chr4:122745600-122746400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:122745600-122746400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:122745600-122747200	Weak transcription	HSMM	muscle
14	chr4:122745600-122747600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:122745600-122748400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:122745600-122748400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:122745600-122748400	Weak transcription	NH-A	brain
18	chr4:122745600-122749000	Weak transcription	NHLF	lung
19	chr4:122745600-122750400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:122745600-122750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:122745600-122750600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:122745600-122750600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:122745600-122750600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:122745600-122750600	Weak transcription	Left Ventricle	heart
25	chr4:122745600-122750800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:122745600-122751800	Weak transcription	Ovary	ovary
27	chr4:122745600-122758000	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:122745600-122758600	Weak transcription	Fetal Kidney	kidney
29	chr4:122745600-122759800	Weak transcription	Fetal Thymus	thymus
30	chr4:122745600-122760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:122745600-122762000	Weak transcription	Aorta	Aorta
32	chr4:122745600-122764000	Weak transcription	Colonic Mucosa	Colon
33	chr4:122745600-122766200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:122745600-122766600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:122745600-122767200	Weak transcription	Esophagus	oesophagus
36	chr4:122745600-122767200	Weak transcription	Right Ventricle	heart
37	chr4:122745600-122767800	Weak transcription	Pancreas	Pancrea
38	chr4:122745600-122767800	Weak transcription	Thymus	Thymus
39	chr4:122745600-122769200	Weak transcription	Hela-S3	cervix
40	chr4:122745600-122770000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr4:122745600-122781600	Weak transcription	Placenta	Placenta
42	chr4:122745600-122790400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:122745600-122790600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:122745600-122790800	Weak transcription	Psoas Muscle	Psoas
45	chr4:122745800-122746400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:122745800-122746400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:122745800-122746400	Enhancers	Duodenum Mucosa	Duodenum
48	chr4:122745800-122746400	Enhancers	Dnd41	blood
49	chr4:122745800-122746600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:122745800-122747400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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