Variant report

Variant	rs4955426
Chromosome Location	chr3:49143438-49143439
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49143044-49143503	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:49143102-49143794	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:49143352-49143542	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:49143329-49144248	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:49143244-49144064	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr3:49143054-49144556	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49143242-49143657	U87	brain:	n/a	n/a
8	POLR2A	chr3:49143242-49143604	U87	brain:	n/a	n/a
9	POLR2A	chr3:49141030-49144468	K562	blood:	n/a	n/a
10	POLR2A	chr3:49143156-49144337	K562	blood:	n/a	n/a
11	POLR2A	chr3:49141134-49145325	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:49143142-49144309	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:49143324-49144292	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49062158..49068430-chr3:49139884..49143886,7	K562	blood:
2	chr3:49051141..49053144-chr3:49141791..49144128,2	MCF-7	breast:
3	chr3:49141891..49144060-chr3:49160282..49161903,2	MCF-7	breast:
4	chr3:49065644..49068081-chr3:49140753..49143557,2	MCF-7	breast:
5	chr3:49130473..49134563-chr3:49139987..49143694,13	MCF-7	breast:
6	chr3:49128213..49133667-chr3:49140039..49144982,11	MCF-7	breast:
7	chr3:49064550..49068051-chr3:49140813..49143886,3	K562	blood:
8	chr3:49140491..49143701-chr3:49201484..49205334,5	K562	blood:
9	chr3:49140554..49145107-chr3:49167346..49172356,7	MCF-7	breast:
10	chr3:49141581..49143765-chr3:49156175..49158476,2	K562	blood:
11	chr3:49141824..49144900-chr3:49147754..49149613,4	K562	blood:
12	chr3:49130342..49133309-chr3:49142749..49145545,2	K562	blood:
13	chr3:49027258..49030137-chr3:49142521..49145382,2	MCF-7	breast:
14	chr3:49130342..49133374-chr3:49140037..49144249,8	K562	blood:
15	chr3:49141210..49144220-chr3:49153234..49156017,3	K562	blood:

No data

Variant related genes	Relation type
QARS	TF binding region
ENSG00000223343	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178467	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000172046	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 33 )

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

rs_ID	r²[population]
rs10154992	0.91[CEU][hapmap]
rs11130181	0.83[EUR][1000 genomes]
rs11130183	0.87[CEU][hapmap]
rs11130186	0.83[CEU][hapmap]
rs13099075	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3087866	0.86[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs4292260	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs4955411	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs4955416	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs4955417	0.91[CEU][hapmap]
rs4955439	0.87[CEU][hapmap]
rs4955443	0.91[CEU][hapmap]
rs4974081	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4974083	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs6446204	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes]
rs6446247	0.84[AMR][1000 genomes]
rs6446256	0.90[CEU][hapmap]
rs6446257	0.86[CEU][hapmap]
rs6769821	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs6772452	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs6778080	0.91[CEU][hapmap]
rs6787808	0.95[CEU][hapmap]
rs6798112	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6803264	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6809851	0.91[CEU][hapmap]
rs7100	0.86[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs7373072	0.95[CEU][hapmap]
rs7429661	0.87[CEU][hapmap]
rs7434187	0.95[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs7619016	0.91[CEU][hapmap]
rs7621347	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7626076	0.91[CEU][hapmap]
rs7653408	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs9834003	0.87[CEU][hapmap]
rs9864243	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs9865051	1.00[CEU][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[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:33)

SNP	Gene	Cis/trans	Tissue	Source
rs4955426	NICN1	cis	cerebellum	SCAN
rs4955426	AMT	cis	Muscle Skeletal	GTEx
rs4955426	WDR6	cis	Nerve Tibial	GTEx
rs4955426	NICN1	cis	parietal	SCAN
rs4955426	AMT	cis	cerebellum	SCAN
rs4955426	NICN1-AS1	cis	Thyroid	GTEx
rs4955426	NCKIPSD	cis	parietal	SCAN
rs4955426	WDR6	cis	cerebellum	SCAN
rs4955426	AMT	cis	Artery Aorta	GTEx
rs4955426	NICN1	cis	Thyroid	GTEx
rs4955426	WDR6	cis	parietal	SCAN
rs4955426	AMT	cis	Artery Tibial	GTEx
rs4955426	DALRD3	cis	parietal	SCAN
rs4955426	AMT	cis	Whole Blood	GTEx
rs4955426	DALRD3	cis	cerebellum	SCAN
rs4955426	QRICH1	cis	cerebellum	SCAN
rs4955426	ZNF589	cis	parietal	SCAN
rs4955426	WDR6	cis	Muscle Skeletal	GTEx
rs4955426	AMT	cis	lymphoblastoid	seeQTL
rs4955426	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4955426	AMT	cis	Esophagus Mucosa	GTEx
rs4955426	AMT	cis	parietal	SCAN
rs4955426	AMT	cis	Adipose Subcutaneous	GTEx
rs4955426	PHF7	cis	parietal	SCAN
rs4955426	AMT	cis	Thyroid	GTEx
rs4955426	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4955426	IQCF1	cis	cerebellum	SCAN
rs4955426	LZTFL1	cis	cerebellum	SCAN
rs4955426	P4HTM	cis	parietal	SCAN
rs4955426	GPX1	cis	parietal	SCAN
rs4955426	AMT	cis	Nerve Tibial	GTEx
rs4955426	AMT	cis	lung	GTEx
rs4955426	TLR9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49141600-49143600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:49141800-49143800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49142600-49143600	Enhancers	Spleen	Spleen
4	chr3:49142800-49143600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:49142800-49143600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:49142800-49143600	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr3:49142800-49143600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:49142800-49143600	Weak transcription	Fetal Thymus	thymus
9	chr3:49142800-49143600	Weak transcription	NHLF	lung
10	chr3:49142800-49143800	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:49142800-49143800	Enhancers	Fetal Heart	heart
12	chr3:49142800-49143800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:49142800-49144000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:49142800-49144000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:49142800-49144200	Weak transcription	Lung	lung
16	chr3:49142800-49144800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:49142800-49144800	Weak transcription	Aorta	Aorta
18	chr3:49142800-49144800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:49142800-49144800	Weak transcription	Thymus	Thymus
20	chr3:49142800-49145200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:49142800-49145600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:49142800-49145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:49142800-49145800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:49142800-49145800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:49142800-49146000	Weak transcription	Ovary	ovary
26	chr3:49142800-49146600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:49142800-49146600	Weak transcription	HSMMtube	muscle
28	chr3:49142800-49146800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:49142800-49146800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:49142800-49146800	Weak transcription	Fetal Kidney	kidney
31	chr3:49142800-49146800	Weak transcription	Stomach Mucosa	stomach
32	chr3:49142800-49146800	Weak transcription	A549	lung
33	chr3:49142800-49147000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:49142800-49147000	Weak transcription	Psoas Muscle	Psoas
35	chr3:49142800-49147000	Weak transcription	Small Intestine	intestine
36	chr3:49142800-49147200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:49142800-49147200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:49142800-49147200	Weak transcription	K562	blood
39	chr3:49142800-49149000	Weak transcription	NHDF-Ad	bronchial
40	chr3:49142800-49149600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:49142800-49156400	Weak transcription	Right Atrium	heart
42	chr3:49142800-49157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:49142800-49157600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:49143000-49143600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:49143000-49143600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:49143000-49143600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:49143000-49143600	Enhancers	Adipose Nuclei	Adipose
48	chr3:49143000-49143600	Enhancers	Pancreas	Pancrea
49	chr3:49143000-49143600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:49143000-49143600	Genic enhancers	Stomach Smooth Muscle	stomach

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