Variant report

Variant	rs12528414
Chromosome Location	chr6:38404801-38404802
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	chr6:38229115..38229659-chr6:38404798..38405463,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11964058	0.92[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12200371	0.91[JPT][hapmap]
rs12524209	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12526608	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12528646	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12528840	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16890682	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16890715	0.92[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16890751	0.82[JPT][hapmap]
rs28587676	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28889620	0.84[ASN][1000 genomes]
rs4236059	0.82[JPT][hapmap]
rs4316001	0.82[JPT][hapmap]
rs4400204	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4454130	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4601125	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58163486	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59594955	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60581943	0.92[EUR][1000 genomes]
rs6912811	0.82[JPT][hapmap]
rs6914430	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6941817	1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7764900	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470889	0.91[JPT][hapmap]
rs9470890	0.82[ASN][1000 genomes]
rs9688895	0.92[EUR][1000 genomes]
rs9689697	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv523561	chr6:38395874-38406736	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12528414	CCL4	trans	brain	seeQTL
rs12528414	PTGS2	trans	brain	seeQTL
rs12528414	ZNF331	trans	brain	seeQTL
rs12528414	KLF4	trans	brain	seeQTL
rs12528414	CCL3	trans	brain	seeQTL
rs12528414	EGR2	trans	brain	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38376800-38411400	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38398800-38413800	Weak transcription	Aorta	Aorta
4	chr6:38400400-38410800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:38402600-38411200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:38403800-38405200	Enhancers	Brain Angular Gyrus	brain
7	chr6:38403800-38405400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:38404200-38405200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:38404400-38405000	Enhancers	A549	lung
10	chr6:38404400-38405200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:38404400-38405200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:38404400-38405200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:38404400-38405200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:38404400-38405200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:38404400-38405200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:38404400-38405200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:38404400-38405200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr6:38404400-38405200	Enhancers	Fetal Muscle Leg	muscle
19	chr6:38404400-38405200	Enhancers	Lung	lung
20	chr6:38404400-38405200	Enhancers	HUVEC	blood vessel
21	chr6:38404400-38405200	Enhancers	NH-A	brain
22	chr6:38404400-38405200	Enhancers	NHEK	skin
23	chr6:38404400-38405200	Enhancers	NHLF	lung
24	chr6:38404400-38405400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:38404600-38405000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:38404600-38405200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:38404600-38405200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:38404600-38405200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:38404600-38405200	Enhancers	Ovary	ovary
30	chr6:38404600-38405200	Enhancers	NHDF-Ad	bronchial
31	chr6:38404600-38405400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:38404800-38405000	Enhancers	HSMM	muscle
33	chr6:38404800-38405200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:38404800-38405200	Enhancers	Brain Hippocampus Middle	brain
35	chr6:38404800-38405200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:38404800-38406200	Enhancers	Fetal Brain Male	brain
37	chr6:38404800-38413800	Weak transcription	Small Intestine	intestine

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