Variant report

Variant	rs6438529
Chromosome Location	chr3:119177956-119177957
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119177270..119179334-chr3:119205994..119208733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163389	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1060569	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13080905	0.98[ASN][1000 genomes]
rs1797839	0.86[ASN][1000 genomes]
rs1900742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919590	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976919	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2030816	0.85[AMR][1000 genomes]
rs2177812	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2873688	0.86[GIH][hapmap]
rs3732413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814397	0.86[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687860	0.98[ASN][1000 genomes]
rs4688005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688008	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688014	0.85[ASN][1000 genomes]
rs6414282	0.96[ASN][1000 genomes]
rs6414283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438528	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438535	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6777535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6778945	0.88[ASN][1000 genomes]
rs6794822	0.96[ASN][1000 genomes]
rs6796970	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727905	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7621259	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628626	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7630587	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289129	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9809155	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836326	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9836627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850447	0.88[ASN][1000 genomes]
rs9867768	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs9873196	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9874480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6438529	C3orf9	cis	multi-tissue	Pritchard
rs6438529	FSTL1	cis	cerebellum	SCAN

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	chr3:119147400-119179200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:119148800-119180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:119149400-119179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:119149400-119181000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:119149400-119181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:119150200-119179000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119150400-119180200	Strong transcription	Fetal Intestine Large	intestine
10	chr3:119150600-119180800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:119152000-119178000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119152000-119179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:119152200-119178800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:119152200-119179400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:119154000-119181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:119158000-119180000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:119158800-119180000	Strong transcription	Adipose Nuclei	Adipose
18	chr3:119158800-119180000	Strong transcription	Dnd41	blood
19	chr3:119159800-119179400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:119159800-119180800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:119160400-119179400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:119160400-119180200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:119160600-119180000	Strong transcription	HUVEC	blood vessel
24	chr3:119160600-119180800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:119160800-119179400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:119161000-119179000	Strong transcription	Liver	Liver
27	chr3:119161000-119180800	Weak transcription	Fetal Brain Male	brain
28	chr3:119161200-119179600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:119161800-119180000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:119161800-119180400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:119162600-119181000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:119162800-119179200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:119163200-119178200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:119163200-119179800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:119163200-119180400	Strong transcription	HSMM	muscle
36	chr3:119163200-119180800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:119163200-119180800	Strong transcription	Placenta	Placenta
38	chr3:119163200-119181000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:119163400-119178600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:119163400-119180400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:119163400-119180800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:119163400-119180800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:119163400-119180800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr3:119163400-119181200	Strong transcription	Fetal Thymus	thymus
45	chr3:119163600-119179000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:119163600-119180400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:119163600-119180600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:119163800-119179800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:119163800-119180800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:119164200-119180800	Strong transcription	Primary B cells from peripheral blood	blood

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