Variant report

Variant	rs16869295
Chromosome Location	chr8:103244599-103244600
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103239162..103241164-chr8:103243127..103246074,2	K562	blood:
2	chr8:101962637..101964695-chr8:103242719..103245503,2	MCF-7	breast:
3	chr8:103236803..103238462-chr8:103242289..103245252,2	MCF-7	breast:
4	chr8:103232033..103234810-chr8:103243383..103246591,3	K562	blood:
5	chr8:103241777..103245132-chr8:103247970..103252049,6	MCF-7	breast:
6	chr8:103238918..103240995-chr8:103242872..103245266,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246263	Chromatin interaction
ENSG00000048392	Chromatin interaction
ENSG00000164924	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1037699	0.82[EUR][1000 genomes]
rs1037700	0.84[EUR][1000 genomes]
rs10505019	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1052069	0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1052071	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11774420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774459	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774772	1.00[GIH][hapmap]
rs11776865	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11777942	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778107	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11783467	0.93[ASN][1000 genomes]
rs11784180	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784534	0.81[ASN][1000 genomes]
rs11785514	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11786397	0.81[ASN][1000 genomes]
rs13261195	1.00[GIH][hapmap]
rs16869269	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs16869276	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869282	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16918482	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2305832	1.00[GIH][hapmap]
rs2387995	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28928571	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28928592	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28928597	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28999671	0.93[ASN][1000 genomes]
rs28999676	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28999706	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29000274	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29000286	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs29000294	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35693157	0.88[EUR][1000 genomes]
rs3735720	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3735721	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3735722	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3907099	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4329248	0.81[ASN][1000 genomes]
rs5005121	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57901015	0.81[ASN][1000 genomes]
rs60604862	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs718165	1.00[GIH][hapmap]
rs7836046	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841131	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv891243	chr8:103219629-103292724	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16869295	NCALD	cis	lymphoblastoid	seeQTL
rs16869295	RRM2B	cis	Muscle Skeletal	GTEx
rs16869295	RRM2B	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103209800-103244800	Weak transcription	Stomach Mucosa	stomach
2	chr8:103215600-103248400	Weak transcription	Psoas Muscle	Psoas
3	chr8:103216200-103247400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:103216400-103245200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:103216400-103246600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr8:103217000-103248400	Weak transcription	Small Intestine	intestine
7	chr8:103217800-103246400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr8:103218000-103246200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr8:103219200-103247600	Weak transcription	Fetal Brain Male	brain
10	chr8:103220400-103248800	Weak transcription	Hela-S3	cervix
11	chr8:103222600-103246000	Strong transcription	Osteobl	bone
12	chr8:103227600-103246800	Strong transcription	Primary B cells from cord blood	blood
13	chr8:103229600-103246800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr8:103229800-103245000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:103231600-103249800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr8:103234600-103250000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr8:103236600-103245800	Strong transcription	HSMMtube	muscle
18	chr8:103237200-103248400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:103237400-103245400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr8:103238200-103248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr8:103238400-103248200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:103238400-103248800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr8:103239400-103244600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr8:103239400-103246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr8:103239600-103244600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr8:103240000-103245400	Strong transcription	NH-A	brain
27	chr8:103240000-103246800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:103240400-103244800	Strong transcription	Adipose Nuclei	Adipose
29	chr8:103240600-103245200	Weak transcription	Fetal Brain Female	brain
30	chr8:103240600-103246800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr8:103240800-103246600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr8:103240800-103247600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr8:103240800-103247600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr8:103240800-103248800	Weak transcription	Pancreas	Pancrea
35	chr8:103240800-103249000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr8:103240800-103249000	Weak transcription	Gastric	stomach
37	chr8:103241000-103244600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:103241000-103245800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr8:103241000-103246600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr8:103241000-103247200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr8:103241000-103248000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr8:103241000-103248200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr8:103241000-103248200	Weak transcription	Aorta	Aorta
44	chr8:103241000-103248400	Weak transcription	Lung	lung
45	chr8:103241000-103248400	Weak transcription	Thymus	Thymus
46	chr8:103241000-103248600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr8:103241000-103248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr8:103241000-103248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr8:103241000-103249000	Weak transcription	Right Ventricle	heart
50	chr8:103241000-103249200	Weak transcription	Colonic Mucosa	Colon

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