Variant report

Variant	rs1991659
Chromosome Location	chr3:88110033-88110034
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	MXI1	chr3:88106676-88110397	SK-N-SH	brain:	n/a	n/a
2	E2F4	chr3:88109982-88110060	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:88109985-88110071	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:87275003..87277561-chr3:88108674..88111646,3	MCF-7	breast:
2	chr3:88106502..88110909-chr3:88195834..88201659,8	MCF-7	breast:
3	chr3:88109216..88112055-chr3:88137682..88139375,2	K562	blood:

Variant related genes	Relation type
CGGBP1	TF binding region
ENSG00000083937	Chromatin interaction
ENSG00000264119	Chromatin interaction
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs1006895	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040319	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1051413	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051436	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063597	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063603	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865625	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495016	0.95[EUR][1000 genomes]
rs12632529	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058811	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13060730	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063511	0.89[ASN][1000 genomes]
rs13067419	0.91[ASN][1000 genomes]
rs13076170	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098157	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049817	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116149	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732776	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3890707	0.86[ASN][1000 genomes]
rs4241551	0.83[ASN][1000 genomes]
rs4257571	0.86[ASN][1000 genomes]
rs4273396	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4276211	0.91[ASN][1000 genomes]
rs4276212	0.90[ASN][1000 genomes]
rs4337654	0.86[ASN][1000 genomes]
rs4368523	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374552	0.86[ASN][1000 genomes]
rs4378991	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384978	0.89[ASN][1000 genomes]
rs4414876	0.86[ASN][1000 genomes]
rs4416403	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429658	0.91[ASN][1000 genomes]
rs4432672	0.89[ASN][1000 genomes]
rs4434168	0.91[ASN][1000 genomes]
rs4438681	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485742	0.89[ASN][1000 genomes]
rs4488864	0.89[ASN][1000 genomes]
rs4501136	0.86[ASN][1000 genomes]
rs4502603	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507280	0.86[ASN][1000 genomes]
rs4518156	0.86[ASN][1000 genomes]
rs4555548	0.89[ASN][1000 genomes]
rs4568164	0.81[ASN][1000 genomes]
rs4580585	0.89[ASN][1000 genomes]
rs4588391	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596173	0.86[ASN][1000 genomes]
rs4611846	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616670	0.94[ASN][1000 genomes]
rs4638995	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858931	0.91[ASN][1000 genomes]
rs4858936	0.82[ASN][1000 genomes]
rs4858981	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858982	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858985	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858992	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858994	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858995	0.94[ASN][1000 genomes]
rs4858998	0.89[ASN][1000 genomes]
rs4858999	0.89[ASN][1000 genomes]
rs4859001	0.82[ASN][1000 genomes]
rs6419867	0.83[ASN][1000 genomes]
rs6551266	0.85[EUR][1000 genomes]
rs6551268	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6551271	0.91[ASN][1000 genomes]
rs6551272	0.89[ASN][1000 genomes]
rs6551273	0.89[ASN][1000 genomes]
rs6551274	0.86[ASN][1000 genomes]
rs6551275	0.86[ASN][1000 genomes]
rs6551277	0.86[ASN][1000 genomes]
rs6551278	0.86[ASN][1000 genomes]
rs6551282	0.86[ASN][1000 genomes]
rs6551283	0.86[ASN][1000 genomes]
rs6551284	0.86[ASN][1000 genomes]
rs6551285	0.81[ASN][1000 genomes]
rs6551286	0.82[ASN][1000 genomes]
rs6551288	0.82[ASN][1000 genomes]
rs6551289	0.82[ASN][1000 genomes]
rs6551291	0.81[ASN][1000 genomes]
rs6767258	0.86[ASN][1000 genomes]
rs6777019	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781333	0.86[ASN][1000 genomes]
rs6782507	0.83[ASN][1000 genomes]
rs6785359	0.86[ASN][1000 genomes]
rs6786788	0.91[ASN][1000 genomes]
rs6787824	0.91[ASN][1000 genomes]
rs6790426	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790629	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791133	0.86[ASN][1000 genomes]
rs6792208	0.94[ASN][1000 genomes]
rs6793783	0.94[ASN][1000 genomes]
rs6796355	0.89[ASN][1000 genomes]
rs6799233	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804818	0.91[ASN][1000 genomes]
rs7427704	0.86[ASN][1000 genomes]
rs7429120	0.86[ASN][1000 genomes]
rs7430158	0.83[ASN][1000 genomes]
rs7433285	0.86[ASN][1000 genomes]
rs7617691	0.86[ASN][1000 genomes]
rs7618080	0.89[ASN][1000 genomes]
rs7618472	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626777	0.91[ASN][1000 genomes]
rs7628689	0.86[ASN][1000 genomes]
rs7630028	0.91[ASN][1000 genomes]
rs7630240	0.86[ASN][1000 genomes]
rs7632123	0.81[ASN][1000 genomes]
rs7633121	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7635996	0.91[ASN][1000 genomes]
rs7639420	0.89[ASN][1000 genomes]
rs7641173	0.81[ASN][1000 genomes]
rs7643923	0.91[ASN][1000 genomes]
rs7648096	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650707	0.91[ASN][1000 genomes]
rs7651641	0.86[ASN][1000 genomes]
rs7651999	0.91[ASN][1000 genomes]
rs7652528	0.82[ASN][1000 genomes]
rs7653652	0.86[ASN][1000 genomes]
rs9310066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310067	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310068	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310072	0.94[ASN][1000 genomes]
rs9310074	0.91[ASN][1000 genomes]
rs9310077	0.86[ASN][1000 genomes]
rs959048	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959049	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959050	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813894	0.86[ASN][1000 genomes]
rs9814057	0.82[ASN][1000 genomes]
rs9821517	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829873	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832011	0.90[ASN][1000 genomes]
rs9834468	0.80[ASN][1000 genomes]
rs9834501	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835178	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835771	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840953	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9841189	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9845776	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846115	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847019	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850892	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851328	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854138	0.86[ASN][1000 genomes]
rs9861398	0.89[ASN][1000 genomes]
rs9864220	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865335	0.86[ASN][1000 genomes]
rs9865578	0.86[ASN][1000 genomes]
rs9865703	0.86[ASN][1000 genomes]
rs9865710	0.86[ASN][1000 genomes]
rs9865990	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866349	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870952	0.91[AFR][1000 genomes]
rs9872602	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879044	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881255	0.94[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
rs1991659	C3orf38	Cis_1M	lymphoblastoid	RTeQTL
rs1991659	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88106200-88110400	Active TSS	HSMMtube	muscle
2	chr3:88106400-88110400	Active TSS	HMEC	breast
3	chr3:88106400-88111400	Active TSS	NHLF	lung
4	chr3:88106400-88111600	Active TSS	Right Atrium	heart
5	chr3:88106600-88110400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:88106600-88111200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr3:88106600-88111200	Active TSS	K562	blood
8	chr3:88106800-88110200	Active TSS	Muscle Satellite Cultured Cells	--
9	chr3:88106800-88110200	Active TSS	NH-A	brain
10	chr3:88106800-88111000	Active TSS	NHDF-Ad	bronchial
11	chr3:88106800-88111200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:88106800-88111200	Active TSS	GM12878-XiMat	blood
13	chr3:88107000-88110200	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:88107200-88110200	Active TSS	HSMM	muscle
15	chr3:88107200-88110400	Active TSS	NHEK	skin
16	chr3:88109000-88110800	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr3:88109000-88110800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:88109000-88111000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:88109000-88111400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:88109200-88110200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:88109200-88110200	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr3:88109200-88110600	Active TSS	HepG2	liver
23	chr3:88109400-88110200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:88109400-88110200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr3:88109400-88110200	Flanking Active TSS	Fetal Heart	heart
26	chr3:88109400-88110200	Flanking Active TSS	Fetal Kidney	kidney
27	chr3:88109400-88110200	Flanking Active TSS	Fetal Lung	lung
28	chr3:88109400-88110800	Flanking Active TSS	Dnd41	blood
29	chr3:88109400-88111000	Weak transcription	Gastric	stomach
30	chr3:88109400-88111200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:88109400-88111600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:88109400-88111600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:88109400-88111600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:88109400-88111800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:88109400-88111800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:88109400-88115000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:88109400-88115000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:88109400-88115400	Weak transcription	Lung	lung
39	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
40	chr3:88109600-88110200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr3:88109600-88110200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:88109600-88110200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:88109600-88110200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:88109600-88110200	Flanking Active TSS	A549	lung
45	chr3:88109600-88110600	Enhancers	Stomach Mucosa	stomach
46	chr3:88109600-88110600	Flanking Active TSS	Osteobl	bone
47	chr3:88109600-88110800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:88109600-88111600	Flanking Active TSS	HUVEC	blood vessel
49	chr3:88109600-88113000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:88109800-88110200	Enhancers	Fetal Brain Male	brain

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