Variant report

Variant	rs2735559
Chromosome Location	chr3:88106618-88106619
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	POLR2A	chr3:88106068-88106909	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:88099949-88108728	K562	blood:	n/a	n/a
3	RUNX3	chr3:88106514-88106897	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:88106592-88106648	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:88106398-88109341	PBDE	blood:	n/a	n/a
6	POLR2A	chr3:88105998-88109414	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:88106372-88108837	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:88090636..88092766-chr3:88106492..88108052,2	MCF-7	breast:
2	chr3:88105942..88108461-chr3:88204357..88206943,2	K562	blood:
3	chr3:88106502..88110909-chr3:88195834..88201659,8	MCF-7	breast:
4	chr3:88104745..88109799-chr3:88197543..88201780,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229729	TF binding region
CGGBP1	TF binding region
ENSG00000163320	Chromatin interaction
ENSG00000179021	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1006896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925988	0.87[ASN][1000 genomes]
rs12493327	1.00[JPT][hapmap]
rs13074910	1.00[CEU][hapmap]
rs13317202	0.87[ASN][1000 genomes]
rs2735556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858934	0.87[ASN][1000 genomes]
rs4858939	0.80[ASN][1000 genomes]
rs4858940	0.80[ASN][1000 genomes]
rs4859003	0.87[ASN][1000 genomes]
rs55883959	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55928667	0.87[ASN][1000 genomes]
rs55932154	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56185750	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56211058	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56246133	0.87[ASN][1000 genomes]
rs6419868	0.87[ASN][1000 genomes]
rs6419869	0.80[ASN][1000 genomes]
rs6551276	0.87[ASN][1000 genomes]
rs6551281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6551287	0.87[ASN][1000 genomes]
rs6551295	0.80[ASN][1000 genomes]
rs73132512	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73132546	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73146085	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146095	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146099	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148006	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7430022	0.87[ASN][1000 genomes]
rs7431968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7432826	0.87[ASN][1000 genomes]
rs7432838	1.00[JPT][hapmap]
rs7610494	0.80[ASN][1000 genomes]
rs7620830	1.00[JPT][hapmap]
rs7650068	0.87[ASN][1000 genomes]
rs9826925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2735559	CGGBP1	cis	uninvolved skin	skin_eQTL
rs2735559	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88099000-88107200	Weak transcription	Small Intestine	intestine
2	chr3:88100200-88106800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:88100800-88106800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:88101600-88106800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:88102000-88106800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:88102000-88106800	Weak transcription	Right Ventricle	heart
7	chr3:88102200-88106800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr3:88103000-88106800	Weak transcription	Colonic Mucosa	Colon
9	chr3:88103000-88107200	Weak transcription	Esophagus	oesophagus
10	chr3:88103200-88106800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:88103800-88106800	Strong transcription	Placenta	Placenta
12	chr3:88104600-88107200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:88105200-88106800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:88105200-88106800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:88105200-88106800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr3:88105200-88106800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:88105200-88106800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:88105200-88106800	Weak transcription	Fetal Stomach	stomach
19	chr3:88105200-88107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:88105200-88107000	Weak transcription	Aorta	Aorta
21	chr3:88105200-88107000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:88105200-88107000	Weak transcription	Ovary	ovary
23	chr3:88105200-88107000	Weak transcription	Psoas Muscle	Psoas
24	chr3:88105200-88107200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:88105200-88107200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:88105200-88107200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:88105200-88107200	Weak transcription	Gastric	stomach
28	chr3:88105200-88107200	Weak transcription	Left Ventricle	heart
29	chr3:88105200-88107200	Weak transcription	Lung	lung
30	chr3:88105200-88107200	Weak transcription	Pancreas	Pancrea
31	chr3:88105200-88107200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:88105200-88107200	Weak transcription	Spleen	Spleen
33	chr3:88105400-88106800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:88105600-88106800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:88105600-88106800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr3:88106000-88106800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:88106000-88106800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:88106000-88106800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:88106000-88106800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr3:88106000-88106800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:88106000-88106800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr3:88106000-88106800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr3:88106000-88106800	Enhancers	Brain Germinal Matrix	brain
44	chr3:88106000-88106800	Enhancers	Fetal Intestine Small	intestine
45	chr3:88106200-88106800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:88106200-88106800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
47	chr3:88106200-88106800	Active TSS	Fetal Brain Female	brain
48	chr3:88106200-88106800	Enhancers	Fetal Heart	heart
49	chr3:88106200-88106800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr3:88106200-88106800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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