Variant report

Variant	rs12350131
Chromosome Location	chr9:116103180-116103181
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr9:116101967-116103212	H1-neurons	neurons:	n/a	chr9:116101969-116101982
2	TCF12	chr9:116102109-116103249	A549	lung:	n/a	n/a
3	MXI1	chr9:116101420-116103308	SK-N-SH	brain:	n/a	n/a
4	CHD1	chr9:116102186-116103262	IMR90	lung:	n/a	n/a
5	HCFC1	chr9:116102262-116103336	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116102720..116107904-chr9:116161009..116164019,5	MCF-7	breast:
2	chr8:21998505..21999349-chr9:116102446..116103218,2	Hela-S3	cervix:
3	chr9:116100085..116103833-chr9:116137751..116140667,4	MCF-7	breast:
4	chr2:232379204..232382044-chr9:116102991..116105023,2	MCF-7	breast:
5	chr9:116099899..116105558-chr9:116170913..116174361,7	MCF-7	breast:
6	chr9:116063977..116066911-chr9:116102342..116104616,4	MCF-7	breast:
7	chr9:116063284..116065510-chr9:116102338..116105750,4	MCF-7	breast:
8	chr9:116101294..116104058-chr9:116110419..116112658,2	K562	blood:
9	chr9:116102456..116104363-chr9:116171276..116174227,4	MCF-7	breast:
10	chr9:116036149..116038435-chr9:116101107..116104521,3	K562	blood:
11	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:

No data

Variant related genes	Relation type
WDR31	TF binding region
ENSG00000148218	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000168476	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10124515	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10481639	0.97[AFR][1000 genomes]
rs10481674	0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs10817477	0.85[ASN][1000 genomes]
rs10981736	0.85[ASN][1000 genomes]
rs10981742	0.97[AFR][1000 genomes]
rs10981754	0.83[ASN][1000 genomes]
rs12684385	0.85[ASN][1000 genomes]
rs13289574	0.83[ASN][1000 genomes]
rs16932583	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs16932806	0.85[ASN][1000 genomes]
rs2296076	0.84[ASN][1000 genomes]
rs28480972	0.82[ASN][1000 genomes]
rs34289746	0.82[ASN][1000 genomes]
rs34294772	0.82[ASN][1000 genomes]
rs34429100	0.83[ASN][1000 genomes]
rs34749539	0.81[ASN][1000 genomes]
rs35275471	0.83[ASN][1000 genomes]
rs35860025	0.82[ASN][1000 genomes]
rs35915957	0.82[ASN][1000 genomes]
rs3810920	0.85[ASN][1000 genomes]
rs5012573	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs61161242	0.82[ASN][1000 genomes]
rs7873862	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7875945	0.89[YRI][hapmap]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12350131	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116101400-116103200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:116101600-116103200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr9:116101600-116103200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:116101600-116103200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:116101600-116103200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:116101600-116103200	Active TSS	Brain Angular Gyrus	brain
7	chr9:116101600-116103200	Active TSS	Colonic Mucosa	Colon
8	chr9:116101600-116103200	Active TSS	Fetal Kidney	kidney
9	chr9:116101600-116103200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr9:116101600-116103200	Active TSS	Right Atrium	heart
11	chr9:116101600-116103200	Active TSS	GM12878-XiMat	blood
12	chr9:116101800-116103200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:116101800-116103200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr9:116101800-116103200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:116101800-116103200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:116101800-116103200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:116101800-116103200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:116101800-116103200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:116101800-116103200	Flanking Active TSS	Liver	Liver
20	chr9:116101800-116103200	Active TSS	Psoas Muscle	Psoas
21	chr9:116101800-116103200	Active TSS	A549	lung
22	chr9:116101800-116103200	Active TSS	NH-A	brain
23	chr9:116102000-116103200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr9:116102000-116103200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:116102000-116103200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:116102000-116103200	Active TSS	Aorta	Aorta
27	chr9:116102000-116103200	Active TSS	Fetal Brain Female	brain
28	chr9:116102000-116103200	Active TSS	Fetal Intestine Large	intestine
29	chr9:116102000-116103200	Active TSS	Fetal Intestine Small	intestine
30	chr9:116102000-116103200	Active TSS	Fetal Lung	lung
31	chr9:116102000-116103200	Active TSS	Fetal Muscle Leg	muscle
32	chr9:116102000-116103200	Active TSS	Fetal Thymus	thymus
33	chr9:116102000-116103200	Active TSS	Ovary	ovary
34	chr9:116102000-116103200	Active TSS	Pancreas	Pancrea
35	chr9:116102000-116103200	Active TSS	Stomach Mucosa	stomach
36	chr9:116102000-116103200	Active TSS	Hela-S3	cervix
37	chr9:116102000-116103200	Active TSS	HSMM	muscle
38	chr9:116102000-116103200	Active TSS	HSMMtube	muscle
39	chr9:116102000-116103200	Active TSS	NHDF-Ad	bronchial
40	chr9:116102000-116103200	Active TSS	NHLF	lung
41	chr9:116102000-116103600	Active TSS	Stomach Smooth Muscle	stomach
42	chr9:116102000-116103800	Active TSS	Rectal Smooth Muscle	rectum
43	chr9:116102200-116103200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:116102200-116103200	Active TSS	Brain Hippocampus Middle	brain
45	chr9:116102200-116103200	Active TSS	Placenta	Placenta
46	chr9:116102200-116103400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:116102400-116103200	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr9:116102400-116103200	Active TSS	Fetal Muscle Trunk	muscle
49	chr9:116102600-116103200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr9:116102600-116103200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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