Variant report

Variant	rs9566421
Chromosome Location	chr13:39980829-39980830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39943129..39945538-chr13:39980519..39982065,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs4941926	0.88[ASW][hapmap];0.89[LWK][hapmap]
rs6650471	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336131	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9315681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9566422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566427	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9566429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576788	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576795	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9566421	KIAA0564	cis	parietal	SCAN
rs9566421	LHFP	cis	lymphoblastoid	seeQTL
rs9566421	FREM2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39972800-39988600	Weak transcription	Fetal Muscle Leg	muscle
2	chr13:39975800-39981000	Weak transcription	Right Ventricle	heart
3	chr13:39975800-39988400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:39975800-39988600	Weak transcription	Right Atrium	heart
5	chr13:39976000-39981000	Weak transcription	Brain Substantia Nigra	brain
6	chr13:39976200-39984000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:39976600-39990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:39977000-39987800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:39977200-39981000	Weak transcription	Left Ventricle	heart
10	chr13:39977200-39983800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr13:39977400-39983600	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:39977600-39982600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr13:39977800-39984400	Weak transcription	Psoas Muscle	Psoas
14	chr13:39979200-39981800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr13:39979400-39981600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr13:39979400-39983600	Weak transcription	Fetal Brain Male	brain
17	chr13:39979600-39981600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr13:39980000-39981000	Weak transcription	Ovary	ovary
19	chr13:39980000-39983600	Weak transcription	Brain Anterior Caudate	brain
20	chr13:39980000-39983600	Weak transcription	Fetal Lung	lung
21	chr13:39980000-39983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:39980000-39983800	Weak transcription	NHDF-Ad	bronchial
23	chr13:39980000-39984000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:39980000-39984000	Weak transcription	NHLF	lung
25	chr13:39980200-39981000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:39980200-39981400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:39980200-39982400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:39980200-39983200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr13:39980200-39983200	Weak transcription	Brain Angular Gyrus	brain
30	chr13:39980200-39983600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr13:39980200-39983600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:39980200-39983800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:39980200-39984400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr13:39980200-39988600	Weak transcription	Fetal Stomach	stomach
35	chr13:39980400-39981400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr13:39980400-39982000	Weak transcription	Fetal Heart	heart
37	chr13:39980400-39983600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr13:39980400-39983800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr13:39980400-39984400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr13:39980800-39981400	Enhancers	NHEK	skin
41	chr13:39980800-39981600	Enhancers	HMEC	breast
42	chr13:39980800-39984600	Weak transcription	HSMM	muscle

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