Variant report

Variant	rs1006896
Chromosome Location	chr3:88104411-88104412
allele	G/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	GATA3	chr3:88104226-88104561	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:88099949-88108728	K562	blood:	n/a	n/a
3	POLR2A	chr3:88104399-88104599	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:88100660-88104556	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:88104108..88106315-chr3:88113746..88116261,2	MCF-7	breast:
2	chr3:88103271..88105916-chr3:88106089..88108668,3	K562	blood:

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

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10858	1.00[AFR][1000 genomes];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]
rs2735559	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]
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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs9865578	0.80[CEU][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1006896	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs1006896	LGALS14	trans	lymphoblastoid	seeQTL
rs1006896	CGGBP1	cis	uninvolved skin	skin_eQTL
rs1006896	ZNF654	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88091200-88104600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:88093800-88106400	Weak transcription	Right Atrium	heart
3	chr3:88095000-88104600	Weak transcription	Spleen	Spleen
4	chr3:88096000-88104600	Weak transcription	Aorta	Aorta
5	chr3:88099000-88107200	Weak transcription	Small Intestine	intestine
6	chr3:88100000-88104600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:88100200-88106800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:88100600-88104600	Weak transcription	Left Ventricle	heart
9	chr3:88100800-88106800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:88101600-88106800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:88101800-88104600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:88101800-88104600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:88102000-88106200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:88102000-88106800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:88102000-88106800	Weak transcription	Right Ventricle	heart
16	chr3:88102200-88106200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:88102200-88106600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:88102200-88106600	Strong transcription	Fetal Thymus	thymus
19	chr3:88102200-88106800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:88102600-88104600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:88102600-88105600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:88102600-88105600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:88102600-88106000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:88102800-88104600	Weak transcription	Brain Germinal Matrix	brain
25	chr3:88102800-88104600	Weak transcription	Lung	lung
26	chr3:88102800-88105400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:88102800-88105400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:88102800-88105800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:88102800-88106000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:88102800-88106200	Strong transcription	NHDF-Ad	bronchial
31	chr3:88103000-88104600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:88103000-88104600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:88103000-88104600	Weak transcription	Fetal Brain Male	brain
34	chr3:88103000-88104600	Weak transcription	Fetal Intestine Small	intestine
35	chr3:88103000-88104600	Weak transcription	Fetal Stomach	stomach
36	chr3:88103000-88104600	Strong transcription	Dnd41	blood
37	chr3:88103000-88105400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:88103000-88105400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:88103000-88105600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:88103000-88106400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:88103000-88106600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:88103000-88106800	Weak transcription	Colonic Mucosa	Colon
43	chr3:88103000-88107200	Weak transcription	Esophagus	oesophagus
44	chr3:88103200-88104600	Weak transcription	Gastric	stomach
45	chr3:88103200-88106800	Weak transcription	Brain Angular Gyrus	brain
46	chr3:88103400-88104600	Strong transcription	GM12878-XiMat	blood
47	chr3:88103400-88105000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:88103400-88105200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:88103400-88105400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:88103400-88105600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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