Variant report

Variant	rs10963890
Chromosome Location	chr9:18977333-18977334
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:18975628..18978246-chr9:18981249..18983402,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10116465	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10116604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10117445	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10119748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10122564	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10811070	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10811096	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811115	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10963851	0.84[ASN][1000 genomes]
rs10963853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap]
rs10963856	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963857	0.84[ASN][1000 genomes]
rs10963858	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10963860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[ASN][1000 genomes]
rs10963861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963873	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10963880	0.82[EUR][1000 genomes]
rs10963882	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10963883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10963886	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10963888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.90[MKK][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963937	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11496354	0.83[ASN][1000 genomes]
rs12115446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12346001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12379525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12380170	0.82[EUR][1000 genomes]
rs16937210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16937322	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17236157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2039007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2039009	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28689789	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28742005	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28805064	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4478656	0.82[EUR][1000 genomes]
rs62560397	1.00[ASN][1000 genomes]
rs62560398	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62560399	0.88[EUR][1000 genomes]
rs62560432	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7031878	1.00[CHB][hapmap]
rs7031911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs7858899	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7873306	0.85[ASN][1000 genomes]
rs883440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657571	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv892699	chr9:18945868-19025693	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1022697	chr9:18951530-19010894	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10963890	CCDC37	trans	brain	seeQTL
rs10963890	ZMYND10	trans	brain	seeQTL
rs10963890	CAPSL	trans	brain	seeQTL
rs10963890	MEIS2	trans	brain	seeQTL
rs10963890	ADORA2A	trans	brain	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18971200-18979400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:18971200-18981600	Weak transcription	Gastric	stomach
3	chr9:18971400-18979200	Weak transcription	Right Ventricle	heart
4	chr9:18971400-18979400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:18975000-18980600	Enhancers	Fetal Thymus	thymus
6	chr9:18975200-18979400	Weak transcription	Lung	lung
7	chr9:18975800-18977400	Enhancers	Fetal Stomach	stomach
8	chr9:18976200-18977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:18976200-18977400	Enhancers	Stomach Mucosa	stomach
10	chr9:18976200-18977400	Flanking Active TSS	Osteobl	bone
11	chr9:18976400-18977400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr9:18976400-18977600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:18976800-18977400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:18976800-18979600	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:18977000-18977400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:18977000-18977400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:18977000-18977400	Enhancers	Duodenum Mucosa	Duodenum
18	chr9:18977000-18977400	Enhancers	Fetal Kidney	kidney
19	chr9:18977000-18977400	Enhancers	Hela-S3	cervix
20	chr9:18977000-18977400	Enhancers	HUVEC	blood vessel
21	chr9:18977000-18977400	Enhancers	NH-A	brain
22	chr9:18977000-18977400	Enhancers	NHLF	lung
23	chr9:18977000-18977600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:18977000-18977600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:18977000-18977600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:18977000-18977600	Enhancers	Fetal Lung	lung
27	chr9:18977000-18977600	Enhancers	Dnd41	blood
28	chr9:18977000-18977800	Enhancers	HSMM	muscle
29	chr9:18977000-18979400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:18977000-18979400	Weak transcription	Ovary	ovary
31	chr9:18977000-18979800	Weak transcription	Fetal Heart	heart
32	chr9:18977000-18980000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:18977000-18981400	Weak transcription	Adipose Nuclei	Adipose
34	chr9:18977000-18981400	Weak transcription	Aorta	Aorta
35	chr9:18977000-18981400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:18977000-18982200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:18977200-18977400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:18977200-18977400	Enhancers	HSMMtube	muscle
39	chr9:18977200-18977600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:18977200-18977800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr9:18977200-18977800	Enhancers	NHDF-Ad	bronchial
42	chr9:18977200-18980200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:18977200-18980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:18977200-18982200	Weak transcription	NHEK	skin

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