Variant report

Variant	rs1046724
Chromosome Location	chr5:178315686-178315687
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	chr5:178310967..178313055-chr5:178314057..178317226,3	MCF-7	breast:
2	chr5:178314966..178317801-chr5:178321245..178325821,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198939	Chromatin interaction
ENSG00000206624	Chromatin interaction
ENSG00000178338	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11249600	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740486	0.83[EUR][1000 genomes]
rs11744810	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745435	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749871	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11955491	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955549	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11956161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516516	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13166562	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13171869	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13182467	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13183468	0.81[EUR][1000 genomes]
rs13189231	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13189941	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1496948	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1566105	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs17652441	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1826863	0.81[EUR][1000 genomes]
rs1845939	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2047356	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34904538	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35245718	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35974815	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35984063	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6600996	0.82[EUR][1000 genomes]
rs6894647	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6897952	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs732531	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap]
rs7445002	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7448421	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7448445	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7722159	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7722441	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953741	0.82[AMR][1000 genomes]

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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1046724	BTNL9	cis	cerebellum	SCAN
rs1046724	TMED9	cis	parietal	SCAN
rs1046724	B4GALT7	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
5	chr5:178296000-178319200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr5:178296200-178319200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:178296400-178317600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr5:178297200-178315800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
9	chr5:178297400-178317400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:178297400-178317400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
11	chr5:178297400-178317400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:178297600-178317400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:178298800-178317800	ZNF genes & repeats	Primary T cells from cord blood	blood
14	chr5:178299000-178317600	ZNF genes & repeats	Fetal Brain Female	brain
15	chr5:178299400-178317400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:178299600-178317400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr5:178299800-178317400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:178299800-178317600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:178301000-178317400	ZNF genes & repeats	Adipose Nuclei	Adipose
20	chr5:178301400-178317200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:178301600-178317600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:178302800-178317600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:178305200-178317000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:178306000-178317600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr5:178306200-178317600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:178306400-178315800	ZNF genes & repeats	Dnd41	blood
27	chr5:178307400-178317600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr5:178307600-178315800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:178307600-178317400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:178307600-178317400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr5:178307600-178317600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
32	chr5:178308400-178322600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr5:178308800-178316000	Strong transcription	Placenta	Placenta
34	chr5:178308800-178316400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:178311200-178316600	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:178311200-178322400	Weak transcription	Hela-S3	cervix
37	chr5:178312200-178317600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
38	chr5:178312400-178315800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
39	chr5:178312400-178315800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
40	chr5:178312400-178317600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr5:178312600-178315800	ZNF genes & repeats	Brain Substantia Nigra	brain
42	chr5:178312600-178316200	ZNF genes & repeats	NH-A	brain
43	chr5:178312800-178317400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:178313200-178315800	Strong transcription	Fetal Intestine Large	intestine
45	chr5:178313200-178316000	Weak transcription	NHLF	lung
46	chr5:178313200-178316400	Weak transcription	Right Ventricle	heart
47	chr5:178313200-178317200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:178313400-178316600	Weak transcription	K562	blood
49	chr5:178313600-178316400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:178313600-178316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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