Variant report

Variant	rs35598865
Chromosome Location	chr16:30438930-30438931
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30437385..30440106-chr20:49377944..49379729,2	MCF-7	breast:
2	chr16:30427757..30432109-chr16:30437396..30442167,10	MCF-7	breast:
3	chr16:30438691..30441643-chr16:30669537..30671666,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156860	Chromatin interaction
ENSG00000199787	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11150586	1.00[JPT][hapmap]
rs11640950	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11646130	1.00[JPT][hapmap]
rs11862806	1.00[JPT][hapmap]
rs11863150	1.00[JPT][hapmap]
rs12165013	0.83[ASN][1000 genomes]
rs12446288	1.00[JPT][hapmap]
rs12447833	0.88[AFR][1000 genomes]
rs12921440	1.00[JPT][hapmap]
rs13333093	1.00[JPT][hapmap]
rs35480350	1.00[JPT][hapmap]
rs3574	1.00[JPT][hapmap]
rs4465620	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4787642	1.00[JPT][hapmap]
rs4787643	1.00[JPT][hapmap]
rs4788409	1.00[JPT][hapmap]
rs4788413	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4788414	0.92[ASN][1000 genomes]
rs6565182	1.00[JPT][hapmap]
rs6565183	1.00[JPT][hapmap]
rs7203359	0.88[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs8045252	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8045570	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8046445	1.00[JPT][hapmap]
rs8049108	1.00[JPT][hapmap]
rs8050812	1.00[JPT][hapmap]
rs8051096	1.00[JPT][hapmap]
rs8060853	1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35598865	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs35598865	ALDOA	cis	cerebellum	SCAN
rs35598865	TBX6	cis	parietal	SCAN
rs35598865	CORO1A	cis	cerebellum	SCAN
rs35598865	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30428800-30440200	Weak transcription	Fetal Heart	heart
2	chr16:30429600-30440200	Weak transcription	NHDF-Ad	bronchial
3	chr16:30429800-30440200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:30429800-30440200	Weak transcription	Fetal Kidney	kidney
5	chr16:30429800-30440200	Weak transcription	HSMMtube	muscle
6	chr16:30429800-30440400	Weak transcription	Right Atrium	heart
7	chr16:30430000-30439400	Weak transcription	Fetal Brain Male	brain
8	chr16:30430000-30440200	Strong transcription	Fetal Intestine Small	intestine
9	chr16:30430000-30440400	Weak transcription	Small Intestine	intestine
10	chr16:30430000-30440600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr16:30430200-30440000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr16:30430200-30440000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr16:30430200-30440200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr16:30430200-30440200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr16:30430200-30440600	Weak transcription	Psoas Muscle	Psoas
16	chr16:30430400-30439000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr16:30430600-30439400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:30430600-30440200	Strong transcription	Fetal Stomach	stomach
19	chr16:30430600-30440400	Weak transcription	Stomach Mucosa	stomach
20	chr16:30431600-30439200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:30431600-30439600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr16:30431600-30439800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr16:30431600-30439800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr16:30431600-30440000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr16:30431600-30440000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:30431800-30440200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr16:30432400-30439200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr16:30432400-30439800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr16:30432800-30439600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr16:30433400-30439400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr16:30434200-30439000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:30434200-30439000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr16:30434800-30439600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr16:30435400-30439400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr16:30435600-30440200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr16:30435800-30440200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr16:30435800-30440200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr16:30436000-30439000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr16:30436000-30439000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr16:30436000-30439000	Weak transcription	HSMM	muscle
41	chr16:30436000-30439600	Weak transcription	Fetal Brain Female	brain
42	chr16:30436000-30440000	Weak transcription	Osteobl	bone
43	chr16:30436000-30440200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr16:30436000-30440200	Weak transcription	Brain Angular Gyrus	brain
45	chr16:30436000-30440200	Weak transcription	Brain Anterior Caudate	brain
46	chr16:30436000-30440200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr16:30436000-30440200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr16:30436000-30440600	Weak transcription	Aorta	Aorta
49	chr16:30436200-30439000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr16:30436200-30439000	Weak transcription	Fetal Intestine Large	intestine

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