Variant report

Variant	rs3828235
Chromosome Location	chr2:55649209-55649210
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	GATA3	chr2:55649179-55649379	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55458950..55461087-chr2:55647562..55649544,2	K562	blood:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10169061	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10169395	0.86[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10172058	0.80[EUR][1000 genomes]
rs10187983	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191937	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10194425	0.90[CHB][hapmap];0.83[YRI][hapmap]
rs1045613	0.80[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap]
rs10496042	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125571	0.83[ASN][1000 genomes]
rs11125573	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11678347	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11886931	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11891739	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs11902837	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614357	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12617887	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12621289	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12621495	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623605	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713293	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12713294	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12713295	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12713296	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12713298	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991401	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13001912	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13010237	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13010255	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13013113	0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13019339	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13022424	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13389156	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13423775	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349884	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1349885	0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1370360	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1370361	0.80[CEU][hapmap]
rs1437394	0.84[YRI][hapmap]
rs1902060	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198575	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2589084	0.81[YRI][hapmap]
rs2589085	0.84[YRI][hapmap]
rs2589087	0.81[YRI][hapmap]
rs2867174	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2867175	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2867176	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2867177	0.81[AMR][1000 genomes]
rs28672687	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2920971	0.84[YRI][hapmap]
rs3111404	0.84[YRI][hapmap]
rs3111413	0.81[YRI][hapmap]
rs36052911	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791642	0.91[CHB][hapmap]
rs3791650	0.95[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs3791652	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56978967	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66882175	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6724338	0.91[CHB][hapmap];0.87[YRI][hapmap]
rs6746104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6747649	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752182	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6754930	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6756777	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74181227	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7558687	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap]
rs7561473	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7569535	0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7572492	0.90[CEU][hapmap];0.96[GIH][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7589390	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7600339	0.82[AMR][1000 genomes]
rs7604067	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7606505	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9789365	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3828235	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL
rs3828235	EML6	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55647800-55652400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55648000-55649400	Enhancers	NHDF-Ad	bronchial
3	chr2:55648000-55649800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:55648000-55649800	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:55648000-55650000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:55648000-55650000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:55648000-55650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:55648000-55650000	Enhancers	Brain Germinal Matrix	brain
9	chr2:55648000-55651000	Weak transcription	HMEC	breast
10	chr2:55648000-55651200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:55648000-55651600	Weak transcription	NHEK	skin
12	chr2:55648000-55652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:55648000-55652200	Weak transcription	HUVEC	blood vessel
14	chr2:55648000-55652200	Weak transcription	NH-A	brain
15	chr2:55648000-55652400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:55648000-55652400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:55648000-55652400	Weak transcription	HSMM	muscle
18	chr2:55648000-55653400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:55648000-55659000	Weak transcription	Adipose Nuclei	Adipose
20	chr2:55648200-55650000	Enhancers	Primary hematopoietic stem cells	blood
21	chr2:55648200-55651000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:55648200-55651200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:55648200-55652200	Weak transcription	Osteobl	bone
24	chr2:55648400-55649400	Enhancers	Primary T cells from cord blood	blood
25	chr2:55648400-55649400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:55648400-55649400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:55648400-55649400	Weak transcription	Dnd41	blood
28	chr2:55648400-55649400	Weak transcription	Hela-S3	cervix
29	chr2:55648400-55649600	Weak transcription	Brain Substantia Nigra	brain
30	chr2:55648400-55650000	Weak transcription	Brain Anterior Caudate	brain
31	chr2:55648400-55650200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:55648400-55651800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:55648400-55652400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:55648400-55652400	Enhancers	A549	lung
35	chr2:55648400-55652400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr2:55648600-55649600	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:55648600-55650000	Weak transcription	Brain Angular Gyrus	brain
38	chr2:55648600-55650400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:55648600-55651000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:55648600-55651200	Weak transcription	K562	blood
41	chr2:55648800-55649400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:55648800-55650000	Weak transcription	GM12878-XiMat	blood
43	chr2:55648800-55650200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:55649000-55650000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:55649200-55649600	Enhancers	Fetal Heart	heart
46	chr2:55649200-55649600	Enhancers	Fetal Lung	lung
47	chr2:55649200-55649600	Weak transcription	HepG2	liver
48	chr2:55649200-55651000	Weak transcription	NHLF	lung

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