Variant report

Variant	rs2071888
Chromosome Location	chr6:33272855-33272856
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
2	chr6:33270764..33273240-chr6:33372859..33374945,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231925	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000237649	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1014779	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1061783	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs120626	0.83[ASN][1000 genomes]
rs1800838	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013891	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071889	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213199	0.80[ASN][1000 genomes]
rs213201	0.80[ASN][1000 genomes]
rs213202	0.80[ASN][1000 genomes]
rs213204	0.80[ASN][1000 genomes]
rs2395379	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2894334	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3106190	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3106195	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130016	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130018	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130099	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130100	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130101	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130102	0.86[EUR][1000 genomes]
rs3130262	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130263	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130264	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130265	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130266	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130267	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130269	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130270	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3130271	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135405	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135407	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135408	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3135409	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446735	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs456261	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs463260	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs464865	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs469064	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474353	0.80[ASN][1000 genomes]
rs9277968	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2071888	TAPBP	cis	Artery Tibial	GTEx
rs2071888	TAPBP	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33268000-33273600	Weak transcription	Stomach Mucosa	stomach
2	chr6:33268200-33273000	Weak transcription	A549	lung
3	chr6:33268200-33279400	Strong transcription	Fetal Intestine Small	intestine
4	chr6:33268200-33279600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:33268200-33279800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:33268200-33279800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:33268200-33279800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:33268200-33279800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:33268200-33279800	Weak transcription	Right Atrium	heart
10	chr6:33268200-33279800	Weak transcription	HSMMtube	muscle
11	chr6:33268400-33279600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:33268400-33279800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:33268600-33273000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:33268600-33279600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:33268600-33279800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:33268600-33279800	Weak transcription	HSMM	muscle
17	chr6:33268800-33279400	Strong transcription	Fetal Thymus	thymus
18	chr6:33268800-33279600	Weak transcription	NH-A	brain
19	chr6:33269000-33273200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:33269000-33274000	Strong transcription	Osteobl	bone
21	chr6:33269000-33274600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr6:33269000-33279800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:33269000-33279800	Weak transcription	Fetal Heart	heart
24	chr6:33269000-33279800	Strong transcription	Fetal Stomach	stomach
25	chr6:33269200-33279000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr6:33269200-33279400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:33269200-33279600	Weak transcription	Fetal Brain Male	brain
28	chr6:33269400-33274400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr6:33269400-33274600	Strong transcription	Liver	Liver
30	chr6:33269400-33274800	Strong transcription	Fetal Intestine Large	intestine
31	chr6:33269400-33274800	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:33269400-33279200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:33269600-33274200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:33269600-33274600	Strong transcription	Thymus	Thymus
35	chr6:33269600-33278400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:33269600-33279400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:33269800-33273000	Strong transcription	GM12878-XiMat	blood
38	chr6:33269800-33273200	Weak transcription	K562	blood
39	chr6:33269800-33273800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr6:33269800-33274200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr6:33269800-33274400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:33269800-33276200	Strong transcription	Dnd41	blood
43	chr6:33269800-33279200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:33269800-33279400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:33270000-33279800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:33270200-33273200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:33270400-33273000	Strong transcription	Psoas Muscle	Psoas
48	chr6:33270400-33274000	Strong transcription	Placenta	Placenta
49	chr6:33270400-33274200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:33270600-33273600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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