Variant report

Variant	rs10967890
Chromosome Location	chr9:27325731-27325732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10217148	0.85[YRI][hapmap]
rs10967889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11506243	1.00[AMR][1000 genomes]
rs12001452	1.00[MEX][hapmap]
rs12337261	0.85[YRI][hapmap]
rs12342167	1.00[AMR][1000 genomes]
rs12342171	1.00[AMR][1000 genomes]
rs12684456	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1019688	chr9:27234184-27356374	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv466337	chr9:27250868-27353460	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv613949	chr9:27250868-27353460	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv892866	chr9:27274370-27332818	Bivalent Enhancer Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10967890	CRY1	trans	lymphoblastoid	seeQTL
rs10967890	ARHGAP32	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27323200-27327200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr9:27323400-27333400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:27323600-27326800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr9:27323600-27327600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:27323600-27329400	Weak transcription	Gastric	stomach
6	chr9:27323600-27337400	Weak transcription	Spleen	Spleen
7	chr9:27323800-27329200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:27324200-27326200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:27324200-27326600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:27324400-27328400	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:27324400-27328600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:27324600-27337800	Weak transcription	Pancreas	Pancrea
13	chr9:27325000-27325800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:27325000-27326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:27325000-27326200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:27325000-27326200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:27325000-27326200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:27325000-27328600	Weak transcription	Fetal Stomach	stomach
19	chr9:27325000-27329800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:27325000-27330000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:27325000-27330200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:27325000-27333000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:27325000-27337400	Weak transcription	Colonic Mucosa	Colon
24	chr9:27325200-27326200	Weak transcription	Ovary	ovary
25	chr9:27325200-27327000	Weak transcription	Fetal Intestine Large	intestine
26	chr9:27325400-27328200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:27325600-27325800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:27325600-27328400	Weak transcription	Brain Substantia Nigra	brain
29	chr9:27325600-27329400	Strong transcription	Primary B cells from cord blood	blood
30	chr9:27325600-27333400	Weak transcription	K562	blood

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