Variant report

Variant	rs7619073
Chromosome Location	chr3:49125652-49125653
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	chr3:49064960..49067040-chr3:49125251..49128695,4	MCF-7	breast:
2	chr3:49124027..49128766-chr3:49129255..49132743,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178035	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000198218	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4955416	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7619073	AMT	cis	Esophagus Mucosa	GTEx
rs7619073	AMT	cis	Artery Aorta	GTEx
rs7619073	NICN1-AS1	cis	Thyroid	GTEx
rs7619073	AMT	cis	lung	GTEx
rs7619073	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7619073	NICN1	cis	Thyroid	GTEx
rs7619073	AMT	cis	Artery Tibial	GTEx
rs7619073	WDR6	cis	Muscle Skeletal	GTEx
rs7619073	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7619073	AMT	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49094600-49128200	Weak transcription	Fetal Brain Male	brain
4	chr3:49095400-49129600	Weak transcription	Stomach Mucosa	stomach
5	chr3:49109000-49126200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:49111800-49129600	Weak transcription	HSMMtube	muscle
7	chr3:49113800-49128400	Weak transcription	Small Intestine	intestine
8	chr3:49113800-49129200	Weak transcription	Psoas Muscle	Psoas
9	chr3:49114400-49126000	Weak transcription	Ovary	ovary
10	chr3:49114400-49126200	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:49114400-49126200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:49114400-49128600	Weak transcription	NHLF	lung
13	chr3:49114400-49129600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:49114400-49129600	Weak transcription	Right Ventricle	heart
15	chr3:49114400-49129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:49114400-49130000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:49114800-49129400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:49115000-49125800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:49115000-49127400	Weak transcription	Brain Substantia Nigra	brain
20	chr3:49115000-49128000	Weak transcription	Pancreas	Pancrea
21	chr3:49115000-49129200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:49115000-49130200	Weak transcription	Aorta	Aorta
23	chr3:49115000-49130600	Weak transcription	Spleen	Spleen
24	chr3:49115200-49126600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:49115200-49127000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:49115200-49129400	Weak transcription	Fetal Brain Female	brain
27	chr3:49115200-49129600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:49115600-49126000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:49115600-49126800	Weak transcription	Brain Angular Gyrus	brain
30	chr3:49115600-49126800	Weak transcription	A549	lung
31	chr3:49115600-49128800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:49115600-49128800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:49115600-49129400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:49115600-49129600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:49115600-49129600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:49115600-49130000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:49115600-49130200	Weak transcription	Esophagus	oesophagus
38	chr3:49115800-49126800	Weak transcription	Hela-S3	cervix
39	chr3:49115800-49126800	Weak transcription	HepG2	liver
40	chr3:49115800-49126800	Weak transcription	HUVEC	blood vessel
41	chr3:49115800-49126800	Weak transcription	Osteobl	bone
42	chr3:49115800-49127000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:49115800-49128000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:49115800-49128200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:49115800-49129600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:49115800-49129600	Weak transcription	K562	blood
47	chr3:49116000-49126800	Weak transcription	NH-A	brain
48	chr3:49116000-49128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:49116000-49128200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:49116000-49129000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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