Variant report

Variant	rs7610519
Chromosome Location	chr3:48746427-48746428
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	chr3:48732590..48735474-chr3:48745317..48746995,2	K562	blood:
2	chr3:48738710..48740222-chr3:48745168..48747934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10865953	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs14018	0.83[EUR][1000 genomes]
rs4858799	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4858800	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858830	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442129	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442131	0.83[EUR][1000 genomes]
rs6766238	0.85[EUR][1000 genomes]
rs6796790	0.85[EUR][1000 genomes]
rs6801211	0.85[EUR][1000 genomes]
rs6806356	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929179	1.00[ASN][1000 genomes]
rs7639370	0.81[EUR][1000 genomes]
rs7641050	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9848268	0.96[EUR][1000 genomes]
rs9859473	0.81[EUR][1000 genomes]
rs9873227	0.85[EUR][1000 genomes]
rs9879978	0.81[EUR][1000 genomes]
rs9882443	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990211	0.83[AFR][1000 genomes];0.85[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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7610519	AMT	cis	lung	GTEx
rs7610519	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7610519	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7610519	NICN1-AS1	cis	Thyroid	GTEx
rs7610519	NCKIPSD	cis	Muscle Skeletal	GTEx
rs7610519	WDR6	cis	Muscle Skeletal	GTEx
rs7610519	NCKIPSD	cis	Nerve Tibial	GTEx
rs7610519	AMT	cis	Artery Tibial	GTEx
rs7610519	AMT	cis	Thyroid	GTEx
rs7610519	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7610519	LEPR	trans	lymphoblastoid	RTeQTL
rs7610519	NICN1	cis	Thyroid	GTEx
rs7610519	AMT	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
2	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
4	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:48737200-48746600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:48738200-48752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:48739800-48750800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:48740400-48746600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48740600-48747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:48741400-48750600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:48741600-48749600	Strong transcription	Primary B cells from cord blood	blood
13	chr3:48741600-48750600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:48741600-48752400	Strong transcription	Fetal Intestine Large	intestine
15	chr3:48741800-48749400	Strong transcription	Fetal Stomach	stomach
16	chr3:48741800-48751800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:48741800-48752400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:48741800-48752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:48742000-48748800	Strong transcription	Thymus	Thymus
20	chr3:48742800-48750000	Strong transcription	Placenta	Placenta
21	chr3:48742800-48750800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:48743000-48749600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:48743000-48752400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:48743000-48753000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:48743600-48746600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:48743600-48750600	Strong transcription	Hela-S3	cervix
27	chr3:48743600-48751200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr3:48743600-48751800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:48743600-48752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:48743800-48747800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:48743800-48752800	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr3:48744600-48746800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:48744600-48747600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:48744600-48747600	Enhancers	Right Atrium	heart
35	chr3:48744600-48749400	Strong transcription	Liver	Liver
36	chr3:48744600-48749600	Strong transcription	HUVEC	blood vessel
37	chr3:48744600-48751000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:48744600-48751200	Genic enhancers	Primary T cells from cord blood	blood
39	chr3:48744800-48746600	Strong transcription	Colon Smooth Muscle	Colon
40	chr3:48744800-48747000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr3:48744800-48750600	Genic enhancers	Brain Germinal Matrix	brain
42	chr3:48745000-48746800	Enhancers	Ovary	ovary
43	chr3:48745000-48747800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:48745200-48746600	Genic enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:48745200-48746600	Enhancers	NHDF-Ad	bronchial
46	chr3:48745200-48746800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr3:48745200-48747000	Genic enhancers	Adipose Nuclei	Adipose
48	chr3:48745200-48747600	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr3:48745200-48747600	Genic enhancers	Brain Anterior Caudate	brain
50	chr3:48745200-48747800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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