Variant report

Variant	rs11729955
Chromosome Location	chr4:15689632-15689633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15689195..15690724-chr4:15706537..15708519,2	K562	blood:
2	chr4:15682706..15688918-chr4:15689234..15693729,6	K562	blood:
3	chr4:15688099..15691851-chr4:15693334..15695870,4	MCF-7	breast:
4	chr4:15686622..15689268-chr4:15689311..15691528,2	K562	blood:
5	chr4:15680881..15687102-chr4:15687861..15693031,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction
ENSG00000237765	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10005305	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008878	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10015827	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10017222	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10025875	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10433813	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11722854	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11723554	1.00[CHB][hapmap]
rs11730088	0.81[CEU][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732953	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11735063	1.00[CHB][hapmap]
rs11947383	0.96[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13134177	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17405811	1.00[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];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17476642	1.00[CHB][hapmap]
rs1786	1.00[CHB][hapmap]
rs28394730	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28604503	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35519415	0.84[EUR][1000 genomes]
rs3756246	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs3756247	1.00[CHB][hapmap]
rs3775956	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4301111	1.00[CHB][hapmap]
rs4396986	1.00[CHB][hapmap]
rs4423870	1.00[CHB][hapmap]
rs4549375	1.00[CHB][hapmap]
rs4554069	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6414764	1.00[CHB][hapmap]
rs6449152	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6815254	1.00[CHB][hapmap]
rs6815296	1.00[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];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6824422	1.00[CHB][hapmap]
rs6826058	1.00[CHB][hapmap]
rs6827406	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6839654	1.00[CHB][hapmap]
rs6848779	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[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7434484	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9994518	0.88[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11729955	BST1	cis	multi-tissue	Pritchard
rs11729955	FGFBP2	cis	lymphoblastoid	seeQTL
rs11729955	LOC285550	cis	multi-tissue	Pritchard
rs11729955	FAM200B	cis	parietal	SCAN
rs11729955	FAM200B	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15684000-15691000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:15684000-15692400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:15684000-15697000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:15684000-15704400	Weak transcription	Left Ventricle	heart
5	chr4:15684400-15692200	Weak transcription	Right Ventricle	heart
6	chr4:15684600-15690800	Weak transcription	HSMMtube	muscle
7	chr4:15684800-15690800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr4:15684800-15691600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:15684800-15691600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:15684800-15692200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:15684800-15692400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:15684800-15693600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:15684800-15694200	Weak transcription	Fetal Brain Male	brain
14	chr4:15684800-15704400	Weak transcription	Aorta	Aorta
15	chr4:15685000-15690600	Weak transcription	Brain Germinal Matrix	brain
16	chr4:15685000-15691400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:15685000-15692000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:15685000-15692000	Weak transcription	Right Atrium	heart
19	chr4:15685000-15693000	Weak transcription	Psoas Muscle	Psoas
20	chr4:15685000-15695800	Weak transcription	Stomach Mucosa	stomach
21	chr4:15685800-15691200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:15685800-15691400	Strong transcription	Fetal Thymus	thymus
23	chr4:15685800-15692000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:15686000-15692200	Weak transcription	Brain Angular Gyrus	brain
25	chr4:15686000-15692400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:15686200-15690000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr4:15686200-15690600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr4:15686400-15690400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:15686400-15690600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:15686400-15691000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:15686400-15691200	Weak transcription	Hela-S3	cervix
32	chr4:15686400-15691400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:15686400-15691800	Weak transcription	HepG2	liver
34	chr4:15686400-15692200	Weak transcription	Small Intestine	intestine
35	chr4:15686400-15692800	Weak transcription	GM12878-XiMat	blood
36	chr4:15686600-15691200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:15686600-15691400	Strong transcription	Fetal Intestine Large	intestine
38	chr4:15686600-15691600	Weak transcription	NHLF	lung
39	chr4:15686600-15704400	Weak transcription	Thymus	Thymus
40	chr4:15686800-15690600	Strong transcription	HUVEC	blood vessel
41	chr4:15686800-15691400	Weak transcription	Brain Substantia Nigra	brain
42	chr4:15687000-15690800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:15687000-15691000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr4:15687000-15691600	Weak transcription	Brain Anterior Caudate	brain
45	chr4:15687000-15692200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:15687200-15690000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:15687200-15690000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr4:15687200-15690400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:15687200-15690800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:15687200-15691400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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