Variant report

Variant	rs6438528
Chromosome Location	chr3:119157138-119157139
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	CUX1	chr3:119156914-119157180	GM12878	blood:	n/a	n/a
2	GATA1	chr3:119156459-119157351	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119155062..119157702-chr3:119181053..119182622,2	MCF-7	breast:
2	chr3:119153754..119155960-chr3:119156052..119158543,2	MCF-7	breast:

Variant related genes	Relation type
TMEM39A	TF binding region
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060569	0.94[ASN][1000 genomes]
rs13080905	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797839	0.85[ASN][1000 genomes]
rs1900742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1919586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1919590	0.98[ASN][1000 genomes]
rs1967621	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1976919	0.94[ASN][1000 genomes]
rs2177812	0.94[ASN][1000 genomes]
rs3732413	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3814397	0.85[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.98[ASN][1000 genomes]
rs4687860	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688005	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688007	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688008	0.94[ASN][1000 genomes]
rs4688012	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4688014	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6414282	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414283	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438529	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6438531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438535	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6777535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778945	0.87[ASN][1000 genomes]
rs6794822	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796970	0.98[ASN][1000 genomes]
rs71618795	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs727905	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7430798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621259	0.94[ASN][1000 genomes]
rs7628626	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7630587	0.98[ASN][1000 genomes]
rs7642502	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9289129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809155	0.98[ASN][1000 genomes]
rs9836627	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9850447	0.87[ASN][1000 genomes]
rs9858137	0.83[AMR][1000 genomes]
rs9867768	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs9873196	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs9874480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9877854	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6438528	C3orf9	cis	multi-tissue	Pritchard
rs6438528	KTELC1	cis	multi-tissue	Pritchard
rs6438528	TEAD2	trans	cerebellum	SCAN
rs6438528	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119147000-119179000	Strong transcription	Osteobl	bone
2	chr3:119147200-119180400	Weak transcription	Stomach Mucosa	stomach
3	chr3:119147400-119157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:119147400-119179200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:119147600-119157200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:119147600-119157400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:119147600-119157400	Strong transcription	Fetal Thymus	thymus
8	chr3:119147800-119157200	Strong transcription	Rectal Smooth Muscle	rectum
9	chr3:119147800-119157400	Strong transcription	Placenta	Placenta
10	chr3:119147800-119157400	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:119147800-119157600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr3:119147800-119157600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr3:119147800-119159400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:119148000-119162200	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:119148200-119157200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:119148200-119157200	Strong transcription	Brain Hippocampus Middle	brain
17	chr3:119148400-119157200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:119148400-119157200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr3:119148400-119157400	Strong transcription	NHDF-Ad	bronchial
20	chr3:119148400-119157600	Strong transcription	HepG2	liver
21	chr3:119148600-119157200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:119148600-119157200	Strong transcription	Brain Substantia Nigra	brain
23	chr3:119148800-119157200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:119148800-119157800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:119148800-119157800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:119148800-119175400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:119148800-119180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:119149000-119157200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:119149200-119157200	Strong transcription	Primary B cells from cord blood	blood
30	chr3:119149200-119157200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:119149200-119157200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:119149200-119159200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:119149200-119161600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr3:119149400-119157200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:119149400-119157400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:119149400-119179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:119149400-119181000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:119149400-119181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:119149600-119172600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:119150000-119157200	Strong transcription	Brain Angular Gyrus	brain
41	chr3:119150000-119162000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:119150200-119157200	Strong transcription	A549	lung
43	chr3:119150200-119157400	Strong transcription	NHEK	skin
44	chr3:119150200-119157800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:119150200-119179000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:119150400-119157800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:119150400-119159600	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:119150400-119160600	Strong transcription	Liver	Liver
49	chr3:119150400-119160800	Strong transcription	GM12878-XiMat	blood
50	chr3:119150400-119180200	Strong transcription	Fetal Intestine Large	intestine

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