Variant report

Variant	rs9880199
Chromosome Location	chr3:17353191-17353192
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	chr3:17352641..17354178-chr3:17468928..17471565,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10510476	0.85[LWK][hapmap]
rs17043406	0.85[LWK][hapmap]
rs17043520	0.85[LWK][hapmap]
rs7650336	1.00[AFR][1000 genomes]
rs9631485	0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs9838780	1.00[AFR][1000 genomes]
rs9841955	1.00[AFR][1000 genomes]
rs9858820	0.85[LWK][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs9864049	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9866815	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][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	nsv876590	chr3:17230884-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2755406	chr3:17237396-17589896	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv869378	chr3:17338236-17576692	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9880199	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17255200-17363800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:17298800-17373000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:17321600-17354200	Weak transcription	Placenta	Placenta
4	chr3:17330600-17355400	Weak transcription	Left Ventricle	heart
5	chr3:17330800-17381400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:17331200-17356000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:17331600-17353200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:17333000-17360400	Weak transcription	GM12878-XiMat	blood
9	chr3:17333400-17357400	Weak transcription	Fetal Intestine Large	intestine
10	chr3:17333400-17357600	Weak transcription	Adipose Nuclei	Adipose
11	chr3:17333400-17363400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:17333400-17372000	Weak transcription	Liver	Liver
13	chr3:17333400-17376000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:17333600-17354600	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:17334600-17355200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:17339400-17442200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:17340600-17362600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:17342200-17354200	Weak transcription	HSMMtube	muscle
19	chr3:17342600-17364400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:17343200-17363600	Weak transcription	Primary T cells from cord blood	blood
21	chr3:17343400-17363200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:17344400-17439000	Weak transcription	Aorta	Aorta
23	chr3:17345800-17364000	Weak transcription	Brain Substantia Nigra	brain
24	chr3:17347800-17364000	Weak transcription	Primary B cells from cord blood	blood
25	chr3:17349400-17364400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:17349600-17357800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:17349600-17364000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:17351800-17355400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:17352000-17377600	Weak transcription	Dnd41	blood
30	chr3:17352200-17356000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:17352200-17357400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:17352200-17370800	Weak transcription	Fetal Lung	lung

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