Variant report

Variant	rs6795658
Chromosome Location	chr3:133904831-133904832
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	chr3:132440220..132442616-chr3:133903194..133905189,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248724	Chromatin interaction
ENSG00000113971	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12493731	0.87[ASW][hapmap];0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs28648514	0.81[EUR][1000 genomes]
rs4234422	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234423	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234426	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241371	1.00[JPT][hapmap]
rs4408870	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447762	0.90[AMR][1000 genomes]
rs4470517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577436	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4634087	0.86[CEU][hapmap]
rs4682655	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682656	0.81[EUR][1000 genomes]
rs4682657	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4682665	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682672	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4854617	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854618	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854619	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854813	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55688777	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56104814	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56205980	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271183	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439459	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439467	0.91[EUR][1000 genomes]
rs6439470	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs6439471	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6764932	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779423	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6783989	0.88[EUR][1000 genomes]
rs6787345	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6791361	0.80[EUR][1000 genomes]
rs6795532	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799962	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71807032	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7431604	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433368	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616326	0.81[EUR][1000 genomes]
rs7627059	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631521	0.88[EUR][1000 genomes]
rs7633386	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634265	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289461	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812346	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843401	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862959	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870797	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs9883217	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs9884008	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6795658	ARMC8	cis	cerebellum	SCAN
rs6795658	IL20RB	cis	parietal	SCAN
rs6795658	EPHB1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133871800-133919200	Weak transcription	K562	blood
2	chr3:133873400-133907400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
5	chr3:133877600-133907400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
7	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
9	chr3:133878400-133907400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:133881800-133908800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:133885600-133907400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:133885600-133919600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:133888400-133923600	Weak transcription	Fetal Heart	heart
14	chr3:133888600-133905400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:133893200-133907200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:133893200-133917400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:133894400-133912600	Weak transcription	Fetal Thymus	thymus
18	chr3:133894800-133907200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:133894800-133912600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:133894800-133917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:133894800-133917800	Weak transcription	Right Ventricle	heart
22	chr3:133894800-133917800	Weak transcription	Thymus	Thymus
23	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
25	chr3:133895000-133910600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:133895000-133914400	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:133895000-133917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:133895000-133917400	Weak transcription	Esophagus	oesophagus
29	chr3:133895000-133917800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:133895000-133918000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:133895000-133918000	Weak transcription	Spleen	Spleen
32	chr3:133895000-133918600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:133895000-133918800	Weak transcription	Aorta	Aorta
34	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:133895000-133950200	Weak transcription	Gastric	stomach
36	chr3:133895200-133905200	Weak transcription	HepG2	liver
37	chr3:133895200-133912400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:133895200-133919600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:133895200-133927200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:133895400-133912600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:133895600-133907000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:133895600-133912600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:133895800-133906400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:133895800-133906800	Weak transcription	Fetal Intestine Small	intestine
46	chr3:133895800-133923400	Weak transcription	Lung	lung
47	chr3:133898600-133919400	Weak transcription	A549	lung
48	chr3:133898800-133916600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:133898800-133916800	Weak transcription	NHEK	skin
50	chr3:133899000-133905800	Weak transcription	Stomach Smooth Muscle	stomach

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