Variant report

Variant	rs6471480
Chromosome Location	chr8:95734714-95734715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95650400..95656999-chr8:95729644..95735467,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104413	Chromatin interaction
ENSG00000261437	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10110480	0.84[JPT][hapmap]
rs1046163	0.83[TSI][hapmap]
rs11786992	0.85[JPT][hapmap]
rs12675372	0.81[TSI][hapmap]
rs12678311	0.81[TSI][hapmap]
rs13258807	0.85[JPT][hapmap]
rs15710	0.83[TSI][hapmap]
rs15726	0.83[TSI][hapmap]
rs1895874	0.90[JPT][hapmap]
rs2288260	0.80[TSI][hapmap]
rs2554399	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2554400	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2554401	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2722884	0.83[TSI][hapmap]
rs2722885	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2722886	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs4008177	0.81[TSI][hapmap]
rs6471464	0.83[TSI][hapmap]
rs6471468	0.83[TSI][hapmap]
rs6471471	0.83[TSI][hapmap]
rs66526872	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7010722	0.83[TSI][hapmap]
rs7812489	0.81[TSI][hapmap]
rs7815731	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7816645	0.91[TSI][hapmap]
rs7829467	0.83[TSI][hapmap]
rs7842716	0.81[TSI][hapmap]
rs9643347	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv611751	chr8:95721435-95742394	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6471480	KIAA1429	cis	cerebellum	SCAN
rs6471480	DPY19L4	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95732800-95739200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:95732800-95739600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr8:95732800-95761400	Weak transcription	Spleen	Spleen
4	chr8:95732800-95780400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr8:95733000-95738800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr8:95733000-95739600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr8:95733000-95744600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:95733000-95747600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr8:95733000-95761600	Weak transcription	Aorta	Aorta
10	chr8:95733000-95784400	Weak transcription	Esophagus	oesophagus
11	chr8:95733000-95803800	Weak transcription	Psoas Muscle	Psoas
12	chr8:95733000-95805200	Weak transcription	Colonic Mucosa	Colon
13	chr8:95733200-95738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:95733200-95738600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr8:95733200-95738800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr8:95733200-95739600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:95733200-95739800	Weak transcription	Primary T cells from cord blood	blood
18	chr8:95733200-95739800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr8:95733200-95739800	Weak transcription	HSMMtube	muscle
20	chr8:95733200-95740000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr8:95733200-95740400	Weak transcription	Stomach Mucosa	stomach
22	chr8:95733200-95744800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr8:95733200-95752000	Weak transcription	Primary B cells from cord blood	blood
24	chr8:95733200-95774600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr8:95733200-95805000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr8:95733400-95738800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr8:95733400-95738800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:95733400-95738800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr8:95733400-95739600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr8:95733400-95739800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr8:95733400-95743600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:95733400-95752000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr8:95733400-95783800	Weak transcription	Gastric	stomach
34	chr8:95733400-95784800	Weak transcription	Small Intestine	intestine
35	chr8:95733600-95735000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr8:95733600-95736800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:95733600-95738800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr8:95733600-95738800	Weak transcription	Adipose Nuclei	Adipose
39	chr8:95733600-95738800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr8:95733600-95738800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr8:95733600-95738800	Weak transcription	Fetal Muscle Leg	muscle
42	chr8:95733600-95738800	Weak transcription	Placenta	Placenta
43	chr8:95733600-95738800	Weak transcription	Fetal Thymus	thymus
44	chr8:95733600-95738800	Weak transcription	Left Ventricle	heart
45	chr8:95733600-95738800	Weak transcription	Lung	lung
46	chr8:95733600-95738800	Weak transcription	HSMM	muscle
47	chr8:95733600-95739000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr8:95733600-95739200	Weak transcription	Fetal Intestine Large	intestine
49	chr8:95733600-95740200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr8:95733600-95751800	Weak transcription	Rectal Mucosa Donor 31	rectum

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