Variant report

Variant	rs959048
Chromosome Location	chr3:88111307-88111308
allele	A/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	FOS	chr3:88110660-88111364	HUVEC	blood vessel:	n/a	chr3:88111274-88111286 chr3:88111321-88111330 chr3:88111275-88111285 chr3:88111275-88111285
2	IRF1	chr3:88110888-88111694	K562	blood:	n/a	chr3:88111199-88111213 chr3:88111202-88111214 chr3:88111440-88111454
3	TBL1XR1	chr3:88111222-88111365	K562	blood:	n/a	n/a
4	E2F4	chr3:88111029-88111414	MCF10A-Er-Src	breast:	n/a	n/a
5	MAZ	chr3:88111013-88111477	K562	blood:	n/a	n/a
6	POLR2A	chr3:88111260-88111893	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:87275003..87277561-chr3:88108674..88111646,3	MCF-7	breast:
2	chr3:88109216..88112055-chr3:88137682..88139375,2	K562	blood:
3	chr3:88106854..88110640-chr3:88110801..88115329,7	K562	blood:

Variant related genes	Relation type
CGGBP1	TF binding region
ENSG00000229729	Chromatin interaction
ENSG00000083937	Chromatin interaction
ENSG00000163320	Chromatin interaction
ENSG00000264119	Chromatin interaction

Extended variants
information (count: 158 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs1006895	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040319	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1051413	0.98[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	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063603	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865625	0.95[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058811	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13060730	0.98[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100870	0.81[AFR][1000 genomes]
rs1991659	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116149	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732776	0.98[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	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4257571	0.86[ASN][1000 genomes]
rs4273396	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4276211	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4276212	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4337654	0.86[ASN][1000 genomes]
rs4368523	0.95[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	0.88[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	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429658	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4432672	0.89[ASN][1000 genomes]
rs4434168	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4438681	0.89[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	0.95[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	0.95[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616670	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4638995	0.93[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858985	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858992	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858994	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858995	0.81[AFR][1000 genomes];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	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6551271	0.81[AFR][1000 genomes];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	0.96[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	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6787824	0.91[ASN][1000 genomes]
rs6790426	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790629	0.87[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	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6793783	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6796355	0.89[ASN][1000 genomes]
rs6799233	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804818	0.81[AFR][1000 genomes];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	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626777	0.81[AFR][1000 genomes];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	0.90[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	0.89[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310067	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310068	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310072	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9310074	0.91[ASN][1000 genomes]
rs9310077	0.86[ASN][1000 genomes]
rs959049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959050	0.98[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	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829873	0.89[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	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840953	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9841189	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9845776	0.89[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	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850892	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851328	0.98[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	0.95[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870952	0.95[AFR][1000 genomes]
rs9872602	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879044	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881255	0.81[AFR][1000 genomes];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
rs959048	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs959048	C3orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88106400-88111400	Active TSS	NHLF	lung
2	chr3:88106400-88111600	Active TSS	Right Atrium	heart
3	chr3:88109000-88111400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:88109400-88111600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:88109400-88111600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:88109400-88111600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:88109400-88111800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:88109400-88111800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:88109400-88115000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:88109400-88115000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:88109400-88115400	Weak transcription	Lung	lung
12	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
13	chr3:88109600-88111600	Flanking Active TSS	HUVEC	blood vessel
14	chr3:88109600-88113000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:88109800-88111600	Enhancers	Liver	Liver
16	chr3:88109800-88112200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:88109800-88112800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr3:88109800-88113000	Weak transcription	Left Ventricle	heart
19	chr3:88109800-88113000	Weak transcription	Ovary	ovary
20	chr3:88109800-88113600	Weak transcription	Placenta	Placenta
21	chr3:88109800-88113800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr3:88109800-88113800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:88109800-88115000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:88109800-88115400	Weak transcription	Fetal Intestine Small	intestine
25	chr3:88110000-88111400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:88110000-88111400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr3:88110000-88111400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr3:88110000-88111600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:88110000-88111600	Enhancers	Primary B cells from cord blood	blood
30	chr3:88110000-88111600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr3:88110000-88111800	Enhancers	Hela-S3	cervix
32	chr3:88110000-88112200	Weak transcription	Psoas Muscle	Psoas
33	chr3:88110000-88112400	Enhancers	Brain Anterior Caudate	brain
34	chr3:88110000-88113200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:88110000-88113400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:88110000-88116600	Weak transcription	Thymus	Thymus
37	chr3:88110000-88118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:88110000-88120400	Weak transcription	Fetal Stomach	stomach
39	chr3:88110000-88120400	Weak transcription	Fetal Thymus	thymus
40	chr3:88110000-88121000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:88110200-88111400	Enhancers	Brain Substantia Nigra	brain
42	chr3:88110200-88111600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr3:88110200-88111600	Enhancers	A549	lung
44	chr3:88110200-88111800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:88110200-88111800	Enhancers	Adipose Nuclei	Adipose
46	chr3:88110200-88111800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:88110200-88112400	Enhancers	Duodenum Mucosa	Duodenum
48	chr3:88110200-88115600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:88110200-88117200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:88110200-88124200	Weak transcription	Fetal Kidney	kidney

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