Variant report

Variant	rs1398270
Chromosome Location	chr8:104067005-104067006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103876318..103877933-chr8:104065159..104067089,2	MCF-7	breast:
2	chr8:103874657..103877422-chr8:104066775..104068511,3	MCF-7	breast:
3	chr8:104065394..104066935-chr8:104066977..104068842,2	MCF-7	breast:
4	chr8:104060413..104065276-chr8:104065920..104070550,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155097	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000253320	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1398271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398272	0.80[YRI][hapmap]
rs1473820	0.90[YRI][hapmap]
rs1512350	0.80[YRI][hapmap]
rs1512351	0.82[CHB][hapmap]
rs17199777	0.82[CHB][hapmap]
rs2132863	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2132864	0.80[YRI][hapmap]
rs2248718	0.81[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2453992	0.90[YRI][hapmap]
rs2453996	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2453997	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2454029	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2454044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454048	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs2515201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515205	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3808549	1.00[ASW][hapmap];0.82[CHB][hapmap]
rs7844885	0.88[MEX][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	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1398270	ATP6V1C1	cis	Whole Blood	GTEx
rs1398270	BAALC	cis	cerebellum	SCAN
rs1398270	KLF10	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104034200-104068800	Weak transcription	Small Intestine	intestine
2	chr8:104034400-104069400	Weak transcription	Esophagus	oesophagus
3	chr8:104034600-104068400	Weak transcription	Right Ventricle	heart
4	chr8:104034800-104074600	Weak transcription	NHEK	skin
5	chr8:104035400-104071200	Weak transcription	Brain Angular Gyrus	brain
6	chr8:104037200-104071400	Weak transcription	Fetal Brain Female	brain
7	chr8:104039000-104069400	Weak transcription	Spleen	Spleen
8	chr8:104040200-104071400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:104040600-104071400	Weak transcription	Pancreas	Pancrea
10	chr8:104043800-104068200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr8:104046000-104068000	Weak transcription	NHLF	lung
12	chr8:104050400-104069200	Weak transcription	Aorta	Aorta
13	chr8:104050400-104086000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr8:104050600-104089600	Weak transcription	Psoas Muscle	Psoas
15	chr8:104050800-104067800	Weak transcription	Brain Substantia Nigra	brain
16	chr8:104050800-104069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr8:104051600-104087400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr8:104052800-104082200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr8:104053000-104068600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr8:104053200-104073000	Weak transcription	Colonic Mucosa	Colon
21	chr8:104053200-104085600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:104053600-104083800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:104053800-104067600	Strong transcription	Primary B cells from cord blood	blood
24	chr8:104054000-104084400	Strong transcription	Fetal Thymus	thymus
25	chr8:104054200-104083400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:104054200-104083800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr8:104054200-104084400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr8:104055200-104087000	Weak transcription	K562	blood
29	chr8:104055400-104069800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr8:104056200-104077000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr8:104056800-104069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:104057000-104084200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:104058400-104067400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr8:104058400-104068000	Weak transcription	Fetal Heart	heart
35	chr8:104058800-104071600	Strong transcription	HSMM	muscle
36	chr8:104058800-104073600	Strong transcription	Dnd41	blood
37	chr8:104058800-104083400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr8:104059000-104067800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr8:104059000-104072800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr8:104059000-104083600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr8:104059200-104072000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr8:104059200-104083600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr8:104059400-104070800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:104059400-104083400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr8:104059400-104083800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr8:104059400-104085200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr8:104059400-104085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr8:104059600-104067400	Strong transcription	Adipose Nuclei	Adipose
49	chr8:104059600-104085400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr8:104059800-104083400	Strong transcription	Duodenum Mucosa	Duodenum

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