Variant report

Variant	rs967552
Chromosome Location	chr4:88087440-88087441
allele	C/G
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	RCOR1	chr4:88087129-88087525	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88086859..88089641-chr4:88141106..88143015,2	K562	blood:

Variant related genes	Relation type
ENSG00000248196	TF binding region
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10001721	0.89[ASN][1000 genomes]
rs10015288	0.89[ASN][1000 genomes]
rs1005808	0.89[ASN][1000 genomes]
rs1037813	1.00[YRI][hapmap]
rs12505327	0.89[ASN][1000 genomes]
rs12505408	0.89[ASN][1000 genomes]
rs12505448	0.86[ASN][1000 genomes]
rs12509389	0.89[ASN][1000 genomes]
rs12509445	0.89[ASN][1000 genomes]
rs12640151	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12645763	0.89[ASN][1000 genomes]
rs12646299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12649293	0.85[CEU][hapmap]
rs1552145	0.86[ASN][1000 genomes]
rs1563799	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17604937	1.00[YRI][hapmap]
rs17668731	1.00[YRI][hapmap]
rs17668952	1.00[YRI][hapmap]
rs17703743	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17754784	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17754933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17755005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28513782	0.89[ASN][1000 genomes]
rs3775230	1.00[ASW][hapmap]
rs4355355	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4693158	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693804	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693805	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61734704	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62306545	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62306548	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62308861	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62308864	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62308866	0.90[ASN][1000 genomes]
rs71607411	0.88[ASN][1000 genomes]
rs7698284	0.85[CEU][hapmap]
rs7698923	0.85[CEU][hapmap]

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	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv879526	chr4:88062611-88087832	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs967552	HELQ	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88055200-88102800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:88056600-88090600	Weak transcription	Brain Angular Gyrus	brain
3	chr4:88058200-88109000	Weak transcription	Lung	lung
4	chr4:88058800-88088400	Weak transcription	Thymus	Thymus
5	chr4:88058800-88092200	Weak transcription	Colonic Mucosa	Colon
6	chr4:88059200-88087800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:88059200-88088000	Weak transcription	Fetal Stomach	stomach
8	chr4:88059200-88100800	Weak transcription	Osteobl	bone
9	chr4:88061400-88109400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:88063000-88090800	Weak transcription	Left Ventricle	heart
11	chr4:88063000-88090800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:88063200-88088400	Weak transcription	Ovary	ovary
13	chr4:88063200-88097400	Weak transcription	Small Intestine	intestine
14	chr4:88063200-88102000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:88063800-88087800	Weak transcription	Primary T cells from cord blood	blood
16	chr4:88064200-88090000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:88064200-88098800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:88064200-88100400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:88064400-88092600	Weak transcription	HUVEC	blood vessel
20	chr4:88065600-88088200	Weak transcription	GM12878-XiMat	blood
21	chr4:88066200-88097200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:88066200-88101000	Weak transcription	HMEC	breast
23	chr4:88066600-88089800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:88066800-88093000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:88067000-88089400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:88067600-88096800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:88068000-88116400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:88073000-88087600	Weak transcription	Adipose Nuclei	Adipose
29	chr4:88073000-88089400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:88073400-88093400	Weak transcription	Fetal Kidney	kidney
31	chr4:88073400-88098200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:88073400-88113000	Weak transcription	NHDF-Ad	bronchial
33	chr4:88073800-88090800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:88074000-88100400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:88074200-88087800	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:88074200-88109400	Weak transcription	Pancreas	Pancrea
37	chr4:88074400-88100400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:88075400-88097800	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:88077200-88111000	Weak transcription	Fetal Brain Male	brain
40	chr4:88077800-88099800	Weak transcription	Psoas Muscle	Psoas
41	chr4:88079200-88091000	Weak transcription	NHEK	skin
42	chr4:88080200-88087800	Weak transcription	Fetal Intestine Small	intestine
43	chr4:88080400-88093600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:88080600-88098600	Weak transcription	NH-A	brain
45	chr4:88080600-88101800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr4:88081200-88090600	Weak transcription	Fetal Brain Female	brain
47	chr4:88081200-88092000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:88081400-88089800	Weak transcription	Hela-S3	cervix
49	chr4:88081400-88096400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr4:88081600-88092400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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