Variant report

Variant	rs2470949
Chromosome Location	chr7:104590780-104590781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:104585526..104588327-chr7:104589037..104591902,3	K562	blood:
2	chr7:104577447..104579593-chr7:104590153..104592409,2	K562	blood:
3	chr7:104590688..104592595-chr7:104595872..104597993,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPK2-2	chr7:104590762-104590979	ENSG00000228393.3

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10266287	0.89[ASN][1000 genomes]
rs10953460	0.87[ASN][1000 genomes]
rs10953468	0.94[JPT][hapmap]
rs1142	0.81[JPT][hapmap]
rs1144	0.94[JPT][hapmap]
rs2192932	0.89[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap]
rs2299304	0.89[GIH][hapmap];0.94[JPT][hapmap]
rs2428161	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs2430484	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430486	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470938	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470939	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470940	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470941	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470942	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470943	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470947	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470948	1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470950	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823752	0.82[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4727614	0.94[ASN][1000 genomes]
rs6948885	0.94[JPT][hapmap]
rs6950620	0.89[GIH][hapmap];0.94[JPT][hapmap]
rs6955349	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6965384	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6967587	0.94[JPT][hapmap]
rs7776707	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs7797912	0.89[GIH][hapmap];0.94[JPT][hapmap]
rs916705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2470949	DNAJB9	cis	cerebellum	SCAN
rs2470949	RINT1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104584600-104619000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:104586400-104591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:104586400-104591200	Enhancers	Primary B cells from peripheral blood	blood
4	chr7:104586800-104596800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:104587000-104591000	Weak transcription	Adipose Nuclei	Adipose
6	chr7:104587000-104592200	Weak transcription	NH-A	brain
7	chr7:104587000-104597000	Weak transcription	Fetal Stomach	stomach
8	chr7:104587000-104597600	Weak transcription	Right Atrium	heart
9	chr7:104587200-104591000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr7:104587200-104591000	Weak transcription	Stomach Mucosa	stomach
11	chr7:104587200-104591200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:104587200-104591200	Weak transcription	NHDF-Ad	bronchial
13	chr7:104587200-104591200	Weak transcription	Osteobl	bone
14	chr7:104587200-104591400	Weak transcription	NHLF	lung
15	chr7:104587200-104591600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:104587200-104592000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:104587200-104592000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr7:104587200-104595600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:104587200-104596800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:104587200-104597000	Weak transcription	Fetal Thymus	thymus
21	chr7:104587200-104599000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:104587200-104600800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr7:104587200-104623600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:104587400-104592000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:104587400-104595800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr7:104587400-104597000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr7:104588000-104597000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:104588800-104596800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr7:104589000-104591200	Enhancers	Primary B cells from cord blood	blood
30	chr7:104589200-104595600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:104589200-104595800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:104589400-104596200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr7:104590400-104591400	Enhancers	Duodenum Mucosa	Duodenum
34	chr7:104590600-104590800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:104590600-104590800	Enhancers	Fetal Kidney	kidney
36	chr7:104590600-104590800	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr7:104590600-104591000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:104590600-104591400	Enhancers	Ovary	ovary
39	chr7:104590600-104591400	Enhancers	Small Intestine	intestine
40	chr7:104590600-104592400	Enhancers	GM12878-XiMat	blood
41	chr7:104590600-104594600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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