Variant report

Variant	rs12548344
Chromosome Location	chr8:100880904-100880905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:100879499..100881995-chr8:100889306..100891477,2	MCF-7	breast:
2	chr8:100880380..100882289-chr8:100885533..100888133,2	K562	blood:
3	chr8:100880536..100883479-chr8:100897737..100899269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164919	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10955222	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1130474	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1130569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1135382	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11987173	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12541837	0.85[ASN][1000 genomes]
rs12544943	0.82[JPT][hapmap]
rs12546882	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12548542	0.83[EUR][1000 genomes]
rs12548840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13253073	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs13259051	0.81[EUR][1000 genomes]
rs13260744	0.97[EUR][1000 genomes]
rs13264726	0.84[ASN][1000 genomes]
rs13265660	0.97[EUR][1000 genomes]
rs13271488	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13274441	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13277184	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap]
rs13280341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2305290	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs34513504	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34830464	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35031559	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35135010	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35769167	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4409375	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs4434590	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4480092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4510829	0.94[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4626565	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62534626	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62534633	0.83[EUR][1000 genomes]
rs6468694	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs6468695	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6468696	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6468697	0.92[ASN][1000 genomes]
rs6984511	0.85[ASN][1000 genomes]
rs7009713	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7015733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7812991	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7824037	0.97[EUR][1000 genomes]
rs7828241	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7831963	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7832488	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7840626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7844439	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][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	nsv1033944	chr8:100737321-100916345	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv1830910	chr8:100791156-101114794	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12548344	VPS13B	Cis_1M	lymphoblastoid	RTeQTL
rs12548344	VPS13B	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:100846400-100903800	Weak transcription	Stomach Mucosa	stomach
2	chr8:100850200-100887600	Weak transcription	Psoas Muscle	Psoas
3	chr8:100858600-100894000	Weak transcription	Fetal Brain Male	brain
4	chr8:100860200-100893000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:100860400-100887000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:100866200-100888000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:100868600-100898400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:100869600-100883600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:100870400-100883200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:100871800-100887600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:100872000-100883800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr8:100872000-100898200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr8:100872200-100884800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr8:100872400-100883400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr8:100872400-100883600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr8:100872400-100884400	Weak transcription	Brain Angular Gyrus	brain
17	chr8:100872400-100884400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr8:100872600-100882800	Weak transcription	K562	blood
19	chr8:100872600-100883200	Weak transcription	Brain Substantia Nigra	brain
20	chr8:100872600-100883600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:100872600-100885000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr8:100872800-100883600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr8:100872800-100883800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr8:100872800-100883800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr8:100872800-100885200	Weak transcription	Hela-S3	cervix
26	chr8:100872800-100903800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr8:100873000-100885800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:100873200-100881400	Weak transcription	Brain Anterior Caudate	brain
29	chr8:100873200-100882600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:100873200-100882800	Weak transcription	Brain Hippocampus Middle	brain
31	chr8:100873200-100883000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr8:100873200-100883200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr8:100873200-100883400	Weak transcription	HMEC	breast
34	chr8:100873200-100885400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr8:100873200-100885400	Weak transcription	NHEK	skin
36	chr8:100873200-100886800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr8:100873400-100881200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr8:100873400-100883400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr8:100873400-100891200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr8:100873600-100881400	Weak transcription	Fetal Kidney	kidney
41	chr8:100873600-100881800	Weak transcription	NH-A	brain
42	chr8:100873600-100883800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr8:100874000-100884800	Weak transcription	HUVEC	blood vessel
44	chr8:100874400-100881400	Weak transcription	Esophagus	oesophagus
45	chr8:100874600-100881000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr8:100874600-100881000	Weak transcription	Spleen	Spleen
47	chr8:100874600-100883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr8:100874600-100883000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr8:100874600-100883800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr8:100874800-100883200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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