Variant report

Variant	rs10116824
Chromosome Location	chr9:2840829-2840830
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2831983..2837089-chr9:2838426..2842467,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNV2-1	chr9:2840592-2841471	ENSG00000234656

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10121671	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10125846	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs10217194	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs10481516	0.81[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs10733432	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10733433	0.84[EUR][1000 genomes]
rs10738791	0.84[CEU][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10757713	0.81[CEU][hapmap]
rs10757715	0.85[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10812719	0.91[GIH][hapmap];0.86[MEX][hapmap]
rs10812770	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10968361	0.85[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11790146	0.81[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs1875440	0.83[EUR][1000 genomes]
rs1875441	0.81[EUR][1000 genomes]
rs2173904	0.81[GIH][hapmap]
rs3739460	0.81[CEU][hapmap]
rs3824350	0.93[CEU][hapmap]
rs3824351	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4439183	0.81[CEU][hapmap];0.98[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4741768	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4741769	0.81[ASW][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap]
rs6476038	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6476047	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][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	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028011	chr9:2759097-2904277	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1022873	chr9:2768825-2863264	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv892083	chr9:2809548-2900651	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10116824	CD274	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2811600-2842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:2819600-2841800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:2828600-2843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:2830000-2842400	Weak transcription	Thymus	Thymus
5	chr9:2830800-2842800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:2834400-2842400	Weak transcription	Fetal Brain Male	brain
7	chr9:2834400-2843000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:2836400-2842600	Weak transcription	Fetal Intestine Small	intestine
9	chr9:2836600-2842800	Weak transcription	Aorta	Aorta
10	chr9:2836800-2842000	Weak transcription	Right Ventricle	heart
11	chr9:2836800-2842200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:2836800-2843200	Weak transcription	Gastric	stomach
13	chr9:2836800-2843400	Weak transcription	Spleen	Spleen
14	chr9:2837200-2841400	Weak transcription	Fetal Brain Female	brain
15	chr9:2837200-2841800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:2837200-2842000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:2837200-2842200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:2837200-2842200	Weak transcription	Fetal Kidney	kidney
19	chr9:2837200-2842200	Weak transcription	Pancreas	Pancrea
20	chr9:2837200-2842600	Weak transcription	Colonic Mucosa	Colon
21	chr9:2837200-2842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:2837200-2843200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:2837200-2843200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:2837200-2843200	Weak transcription	Esophagus	oesophagus
25	chr9:2837200-2843200	Weak transcription	Lung	lung
26	chr9:2837400-2841800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:2837400-2842000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:2837400-2842200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:2837400-2842200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:2837400-2842200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:2837400-2842200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr9:2837400-2842200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:2837400-2842200	Weak transcription	Fetal Intestine Large	intestine
34	chr9:2837400-2842400	Weak transcription	Primary B cells from cord blood	blood
35	chr9:2837400-2842800	Weak transcription	Placenta	Placenta
36	chr9:2837400-2842800	Weak transcription	Fetal Thymus	thymus
37	chr9:2837400-2842800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:2837400-2843000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr9:2837400-2843000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr9:2837400-2843200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:2837400-2843200	Weak transcription	Left Ventricle	heart
42	chr9:2837800-2841800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:2837800-2841800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:2837800-2842800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr9:2838200-2841800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr9:2838200-2842000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:2838200-2842000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:2838400-2841800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:2838400-2842000	Enhancers	NHEK	skin
50	chr9:2838400-2842800	Enhancers	Cortex derived primary cultured neurospheres	brain

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