Variant report

Variant	rs3907923
Chromosome Location	chr11:9907037-9907038
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	chr11:9901256..9903580-chr11:9906386..9907985,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10770071	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840318	0.89[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042533	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042540	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12272416	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1398499	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1512829	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap]
rs1828639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403224	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4409812	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910072	0.89[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6483804	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7108583	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7119074	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs7124727	0.86[TSI][hapmap]
rs7128275	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9667075	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9919621	0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS 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	40 gene(s)	inside rSNPs	diseases
2	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3907923	CSF2RB	trans	lymphoblastoid	seeQTL
rs3907923	NLRP10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878400-9916200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
3	chr11:9880200-9913200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:9880600-9914800	Weak transcription	Placenta	Placenta
5	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
6	chr11:9890600-9915200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:9891400-9916800	Weak transcription	Primary B cells from cord blood	blood
8	chr11:9891800-9916600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:9892200-9914600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:9892400-9914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:9892400-9914600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:9892400-9921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:9894000-9910600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:9894200-9915200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:9894400-9907400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:9894400-9916600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
18	chr11:9897000-9915000	Weak transcription	HSMMtube	muscle
19	chr11:9897400-9909000	Weak transcription	Psoas Muscle	Psoas
20	chr11:9897800-9910000	Weak transcription	Fetal Kidney	kidney
21	chr11:9898200-9914800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:9898200-9917000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:9898400-9913800	Weak transcription	Fetal Stomach	stomach
24	chr11:9898600-9914800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:9898800-9915200	Weak transcription	Fetal Intestine Small	intestine
26	chr11:9899400-9915000	Weak transcription	Liver	Liver
27	chr11:9900600-9915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:9901200-9915000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr11:9901200-9916600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:9902200-9917400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:9902400-9913000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:9903400-9915000	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:9903600-9915200	Weak transcription	Ovary	ovary
34	chr11:9903600-9916600	Weak transcription	Fetal Lung	lung
35	chr11:9903800-9909000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:9903800-9914600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:9905800-9907400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:9906000-9915000	Weak transcription	Fetal Intestine Large	intestine
40	chr11:9906200-9907400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:9906400-9908200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:9906400-9912800	Weak transcription	NHLF	lung
43	chr11:9906400-9914800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:9906400-9915000	Weak transcription	Osteobl	bone
45	chr11:9906600-9908200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:9906600-9908200	Weak transcription	NHDF-Ad	bronchial
47	chr11:9906600-9908800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:9906800-9908400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:9906800-9920400	Weak transcription	HUVEC	blood vessel
50	chr11:9907000-9914800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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