Variant report

Variant	rs4289816
Chromosome Location	chr8:9608096-9608097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11773928	0.84[ASN][1000 genomes]
rs11774818	0.87[CEU][hapmap];0.93[CHB][hapmap]
rs11775432	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs11776105	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11780274	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap]
rs11991483	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11991547	0.88[CEU][hapmap];0.80[CHB][hapmap]
rs11994018	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs13250838	0.82[CEU][hapmap]
rs13259379	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13261385	0.88[CEU][hapmap];0.80[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs13264510	0.87[CEU][hapmap];0.81[ASN][1000 genomes]
rs13265363	0.87[CHB][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs13274310	0.82[CEU][hapmap]
rs1393	0.88[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs17734024	0.94[TSI][hapmap]
rs28711551	0.81[ASN][1000 genomes]
rs34308976	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34422213	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34638769	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35017872	0.82[AMR][1000 genomes]
rs35331854	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35341965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35435260	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35617208	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36092720	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4128324	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[TSI][hapmap]
rs4272381	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs4535743	0.87[CHB][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap]
rs4551359	0.82[CEU][hapmap]
rs4570159	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs4840432	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs4841186	0.88[CEU][hapmap];0.93[CHB][hapmap]
rs4841195	0.87[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4841198	0.89[ASN][1000 genomes]
rs58391561	0.85[ASN][1000 genomes]
rs7013834	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.94[TSI][hapmap]
rs7013960	0.83[LWK][hapmap]
rs7015700	0.81[MEX][hapmap]
rs71516530	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71516531	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71516533	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71516535	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71516536	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7839648	0.88[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4289816	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9550000-9627600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr8:9551200-9610600	Weak transcription	Fetal Brain Male	brain
3	chr8:9557400-9632200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:9560600-9609200	Weak transcription	K562	blood
5	chr8:9561000-9616200	Weak transcription	Brain Substantia Nigra	brain
6	chr8:9564000-9608200	Weak transcription	Colonic Mucosa	Colon
7	chr8:9565000-9616200	Weak transcription	Pancreas	Pancrea
8	chr8:9566000-9639400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr8:9567800-9611200	Weak transcription	NHEK	skin
10	chr8:9570000-9638600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr8:9576000-9611400	Weak transcription	Fetal Heart	heart
12	chr8:9585200-9627600	Weak transcription	Hela-S3	cervix
13	chr8:9586800-9609200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:9588600-9626000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr8:9593000-9611200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr8:9593200-9610200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr8:9593800-9610200	Weak transcription	Psoas Muscle	Psoas
18	chr8:9597600-9617000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:9598800-9610200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr8:9599200-9611200	Weak transcription	Fetal Kidney	kidney
21	chr8:9602800-9612400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:9603000-9638800	Weak transcription	Stomach Mucosa	stomach
23	chr8:9604200-9616400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr8:9604200-9637200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:9604800-9611800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr8:9604800-9612200	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr8:9604800-9612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr8:9604800-9613400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr8:9604800-9613800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr8:9604800-9617000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr8:9604800-9617000	Strong transcription	Dnd41	blood
32	chr8:9605000-9608800	Strong transcription	HSMM	muscle
33	chr8:9605000-9611800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr8:9605000-9612200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr8:9605000-9612400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr8:9605000-9614000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr8:9605000-9617000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr8:9605000-9617000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr8:9605000-9617200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr8:9605200-9611800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr8:9605200-9612400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr8:9605200-9613800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr8:9605200-9617000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:9605200-9617200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr8:9605400-9608200	Strong transcription	NHDF-Ad	bronchial
46	chr8:9605400-9608400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr8:9605400-9608600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr8:9605400-9609400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr8:9605400-9609600	Strong transcription	NHLF	lung
50	chr8:9605400-9610600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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