Variant report

Variant	rs4840437
Chromosome Location	chr8:9606264-9606265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9606177..9606904-chr8:9688214..9688998,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10087073	0.81[CHB][hapmap]
rs10094989	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10095004	0.86[CHB][hapmap]
rs10099122	0.85[EUR][1000 genomes]
rs10101132	0.82[CHB][hapmap];0.88[MEX][hapmap]
rs10102170	0.86[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10104032	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10106040	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10111376	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249934	0.82[GIH][hapmap];0.94[TSI][hapmap]
rs11776236	0.86[YRI][hapmap]
rs11778555	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11779335	0.88[LWK][hapmap];0.92[MKK][hapmap]
rs11782886	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11785923	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12114661	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12155819	1.00[ASW][hapmap];0.83[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12542457	0.89[ASW][hapmap];0.83[CEU][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12542912	0.83[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12543959	0.80[YRI][hapmap]
rs12544371	0.83[YRI][hapmap]
rs12545912	0.84[MKK][hapmap]
rs12677313	0.86[YRI][hapmap]
rs12679180	0.86[YRI][hapmap]
rs12679956	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12682175	0.82[YRI][hapmap]
rs13250951	0.86[YRI][hapmap]
rs13260526	0.86[YRI][hapmap]
rs13263409	0.83[YRI][hapmap]
rs13264850	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13270518	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs13272424	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13276086	0.83[ASW][hapmap];0.85[GIH][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1394	0.89[ASW][hapmap];0.82[GIH][hapmap];0.82[LWK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap]
rs35316422	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35874762	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4075359	0.87[CEU][hapmap]
rs4129360	0.82[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4383974	0.82[CHB][hapmap]
rs4612345	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4840426	1.00[ASW][hapmap];0.80[GIH][hapmap];0.82[YRI][hapmap]
rs4841196	0.91[MKK][hapmap]
rs4841203	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4841204	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6601340	0.86[TSI][hapmap]
rs6601350	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67711814	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6982148	0.83[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6989782	0.83[CHB][hapmap];0.80[MEX][hapmap]
rs6990300	0.83[ASW][hapmap];0.81[GIH][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap]
rs6992666	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6994574	0.83[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7001832	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7003791	0.84[YRI][hapmap]
rs7004915	0.87[CHB][hapmap]
rs7006003	0.87[CHB][hapmap]
rs7006985	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7009721	0.87[CHB][hapmap];0.80[MEX][hapmap]
rs7014007	0.87[CHB][hapmap];0.88[MEX][hapmap]
rs7014663	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7459728	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs7461939	0.83[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7462070	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7462910	0.88[LWK][hapmap];0.92[MKK][hapmap]
rs7842207	0.86[CHB][hapmap]
rs7845986	0.86[CHB][hapmap]
rs9644704	0.84[LWK][hapmap];0.80[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9644707	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9650639	0.83[YRI][hapmap]
rs9657509	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4840437	CLDN23	cis	multi-tissue	Pritchard
rs4840437	MFHAS1	cis	cerebellum	SCAN
rs4840437	DEFB134	cis	cerebellum	SCAN
rs4840437	PRSS55	cis	cerebellum	SCAN
rs4840437	C8orf79	cis	parietal	SCAN
rs4840437	PPP1R3B	cis	lymphoblastoid	seeQTL
rs4840437	TNKS	cis	parietal	SCAN
rs4840437	FLJ10661	cis	cerebellum	SCAN
rs4840437	C8orf13	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9529600-9606400	Weak transcription	Esophagus	oesophagus
2	chr8:9535000-9608000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr8:9542200-9606800	Weak transcription	Small Intestine	intestine
4	chr8:9543400-9606400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:9550000-9627600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr8:9551200-9610600	Weak transcription	Fetal Brain Male	brain
7	chr8:9557400-9632200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:9560600-9609200	Weak transcription	K562	blood
9	chr8:9561000-9616200	Weak transcription	Brain Substantia Nigra	brain
10	chr8:9562200-9608000	Weak transcription	Colon Smooth Muscle	Colon
11	chr8:9564000-9608200	Weak transcription	Colonic Mucosa	Colon
12	chr8:9565000-9606400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:9565000-9608000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:9565000-9616200	Weak transcription	Pancreas	Pancrea
15	chr8:9566000-9639400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr8:9567800-9611200	Weak transcription	NHEK	skin
17	chr8:9570000-9638600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr8:9576000-9611400	Weak transcription	Fetal Heart	heart
19	chr8:9579400-9607200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr8:9585200-9627600	Weak transcription	Hela-S3	cervix
21	chr8:9586800-9609200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:9588600-9626000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:9593000-9607400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:9593000-9611200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:9593200-9606400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr8:9593200-9607200	Weak transcription	Right Ventricle	heart
27	chr8:9593200-9610200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr8:9593600-9606600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr8:9593800-9606400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr8:9593800-9608000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr8:9593800-9610200	Weak transcription	Psoas Muscle	Psoas
32	chr8:9594000-9607600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr8:9597600-9617000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:9597800-9606400	Weak transcription	Spleen	Spleen
35	chr8:9598800-9610200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr8:9599200-9611200	Weak transcription	Fetal Kidney	kidney
37	chr8:9602200-9607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr8:9602800-9612400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr8:9603000-9638800	Weak transcription	Stomach Mucosa	stomach
40	chr8:9604200-9616400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr8:9604200-9637200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:9604800-9611800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr8:9604800-9612200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr8:9604800-9612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr8:9604800-9613400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr8:9604800-9613800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr8:9604800-9617000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:9604800-9617000	Strong transcription	Dnd41	blood
49	chr8:9605000-9608800	Strong transcription	HSMM	muscle
50	chr8:9605000-9611800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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