Variant report

Variant	rs4974486
Chromosome Location	chr3:134079528-134079529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr3:134079357-134079890	A549	lung:	n/a	n/a
2	POLR2A	chr3:134079491-134079790	Hela-S3	cervix:	n/a	n/a
3	FOXA1	chr3:134079497-134079737	HepG2	liver:	n/a	chr3:134079634-134079649
4	POLR2A	chr3:134078914-134079730	SK-N-SH	brain:	n/a	n/a
5	FOXA1	chr3:134079381-134079735	HepG2	liver:	n/a	chr3:134079634-134079649
6	NFIC	chr3:134079488-134080443	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:134077759-134079853	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr3:134075038-134079875	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:134074939-134079826	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr3:134078326-134079657	HUVEC	blood vessel:	n/a	n/a
11	FOXA2	chr3:134079351-134079969	A549	lung:	n/a	n/a
12	POLR2A	chr3:134077737-134079796	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
14	POLR2A	chr3:134075092-134079606	A549	lung:	n/a	n/a
15	POLR2A	chr3:134079063-134079789	HUVEC	blood vessel:	n/a	n/a
16	GATA3	chr3:134079433-134079846	T-47D	breast:	n/a	n/a
17	POLR2A	chr3:134075008-134079572	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
19	FOXA2	chr3:134079516-134079719	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
21	FOXA1	chr3:134079449-134079722	HepG2	liver:	n/a	chr3:134079634-134079649
22	GATA3	chr3:134079478-134079850	T-47D	breast:	n/a	n/a
23	POLR2A	chr3:134074967-134094367	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr3:134079057-134079712	U87	brain:	n/a	n/a
25	POLR2A	chr3:134074945-134079788	H1-hESC	embryonic stem cell:	n/a	n/a
26	FOXA1	chr3:134079410-134079783	T-47D	breast:	n/a	chr3:134079634-134079649
27	EP300	chr3:134079439-134079829	T-47D	breast:	n/a	n/a
28	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a
29	FOXA1	chr3:134079402-134079777	T-47D	breast:	n/a	chr3:134079634-134079649
30	POLR2A	chr3:134075053-134079865	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134046165..134047037-chr3:134079239..134080512,3	MCF-7	breast:
2	chr3:134077067..134080470-chr3:134177227..134178995,3	MCF-7	breast:
3	chr3:134079471..134081511-chr3:134198648..134200784,2	MCF-7	breast:
4	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:

Variant related genes	Relation type
RPL39P5	TF binding region
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1111516	1.00[JPT][hapmap]
rs11719057	1.00[JPT][hapmap]
rs1353776	1.00[JPT][hapmap]
rs1466827	1.00[JPT][hapmap]
rs2400278	1.00[JPT][hapmap]
rs2400279	1.00[JPT][hapmap]
rs3732852	1.00[JPT][hapmap]
rs3773820	1.00[JPT][hapmap]
rs3821705	1.00[JPT][hapmap]
rs4264700	1.00[JPT][hapmap]
rs4974494	1.00[JPT][hapmap]
rs4974495	1.00[JPT][hapmap]
rs4974496	1.00[JPT][hapmap]
rs4974498	1.00[JPT][hapmap]
rs6439477	1.00[JPT][hapmap]
rs6439478	1.00[JPT][hapmap]
rs9853621	1.00[JPT][hapmap]

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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv3402332	chr3:134077812-134080610	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4974486	NMNAT3	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
3	chr3:134070000-134082400	Genic enhancers	Right Ventricle	heart
4	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:134071000-134082600	Genic enhancers	NHLF	lung
6	chr3:134071000-134088800	Enhancers	Right Atrium	heart
7	chr3:134071200-134082400	Genic enhancers	Brain Substantia Nigra	brain
8	chr3:134071600-134082200	Weak transcription	Primary T cells from cord blood	blood
9	chr3:134071600-134082800	Genic enhancers	Placenta	Placenta
10	chr3:134072000-134082800	Genic enhancers	Lung	lung
11	chr3:134072200-134082400	Genic enhancers	Brain Hippocampus Middle	brain
12	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
14	chr3:134072600-134080200	Weak transcription	Small Intestine	intestine
15	chr3:134072600-134082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:134072600-134082200	Genic enhancers	Adipose Nuclei	Adipose
17	chr3:134072800-134081000	Genic enhancers	Placenta Amnion	Placenta Amnion
18	chr3:134072800-134082400	Genic enhancers	Brain Cingulate Gyrus	brain
19	chr3:134072800-134082600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
21	chr3:134073000-134080400	Genic enhancers	Ovary	ovary
22	chr3:134073000-134082200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:134073000-134089400	Genic enhancers	HMEC	breast
24	chr3:134073200-134082000	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr3:134073200-134082200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:134073400-134082200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:134073800-134082400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:134074400-134082600	Genic enhancers	Brain Anterior Caudate	brain
30	chr3:134074400-134089400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:134075000-134090400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:134075200-134081000	Genic enhancers	Gastric	stomach
33	chr3:134075200-134082200	Genic enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:134075200-134082400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:134075200-134082800	Genic enhancers	Brain Angular Gyrus	brain
36	chr3:134075600-134082200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:134075800-134079600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:134075800-134079800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
39	chr3:134075800-134082200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:134075800-134082400	Genic enhancers	HSMMtube	muscle
41	chr3:134075800-134082600	Genic enhancers	Rectal Smooth Muscle	rectum
42	chr3:134076000-134079600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:134076000-134081000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:134076200-134079600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:134076200-134079600	Genic enhancers	HUVEC	blood vessel
46	chr3:134076200-134080600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:134076800-134082200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:134076800-134082200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:134076800-134082400	Genic enhancers	HSMM	muscle
50	chr3:134076800-134082600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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