Variant report

Variant	rs10174838
Chromosome Location	chr2:55241216-55241217
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:55241048-55241557	HCT-116	colon:	n/a	n/a
2	CTCF	chr2:55241140-55241290	RPTEC	kidney:	n/a	n/a
3	CTCF	chr2:55241035-55241528	MCF-7	breast:	n/a	n/a
4	CTCF	chr2:55241053-55241459	GM12878	blood:	n/a	n/a
5	CTCF	chr2:55241200-55241350	GM06990	blood:	n/a	n/a
6	CTCF	chr2:55241200-55241350	HCPEpiC	choroid plexus:	n/a	n/a
7	RAD21	chr2:55241121-55241343	K562	blood:	n/a	n/a
8	CTCF	chr2:55241120-55241270	NHDF-neo	bronchial:	n/a	n/a
9	RAD21	chr2:55241172-55241365	K562	blood:	n/a	n/a
10	CTCF	chr2:55241178-55241363	Pancreas_OC	pancreas:	n/a	n/a
11	CTCF	chr2:55241208-55241356	GM10248	blood:	n/a	n/a
12	CTCF	chr2:55241160-55241310	HPAF	blood vessel:	n/a	n/a
13	RAD21	chr2:55241127-55241400	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr2:55241180-55241330	AG10803	skin:	n/a	n/a
15	CTCF	chr2:55241184-55241332	Hela-S3	cervix:	n/a	n/a
16	ZNF143	chr2:55241102-55241425	GM12878	blood:	n/a	n/a
17	RAD21	chr2:55241061-55241382	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:55222320-55241658	K562	blood:	n/a	n/a
19	CTCF	chr2:55241208-55241315	Spleen_OC	spleen:	n/a	n/a
20	RAD21	chr2:55241103-55241435	GM12878	blood:	n/a	n/a
21	CTCF	chr2:55241187-55241358	GM12878	blood:	n/a	n/a
22	CTCF	chr2:55241158-55241388	Medullo	brain:	n/a	n/a
23	CTCF	chr2:55241205-55241346	GM13977	blood:	n/a	n/a
24	CTCF	chr2:55241180-55241330	AoAF	blood vessel:	n/a	n/a
25	RAD21	chr2:55241095-55241436	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr2:55241160-55241310	GM12873	blood:	n/a	n/a
27	RAD21	chr2:55241133-55241384	HepG2	liver:	n/a	n/a
28	RAD21	chr2:55241038-55241376	HepG2	liver:	n/a	n/a
29	CTCF	chr2:55241080-55241230	HCM	heart:	n/a	n/a
30	CTCF	chr2:55241120-55241270	GM12878	blood:	n/a	n/a
31	CTCF	chr2:55241180-55241330	HPF	lung:	n/a	n/a
32	CTCF	chr2:55241203-55241373	LNCaP	prostate:	n/a	n/a
33	RAD21	chr2:55241114-55241400	A549	lung:	n/a	n/a
34	CTCF	chr2:55241160-55241310	HMEC	breast:	n/a	n/a
35	CTCF	chr2:55241215-55241346	K562	blood:	n/a	n/a
36	RAD21	chr2:55241008-55241409	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr2:55241208-55241363	LNCaP	prostate:	n/a	n/a
38	CTCF	chr2:55241140-55241290	BJ	skin:	n/a	n/a
39	RAD21	chr2:55240770-55241573	SK-N-SH	brain:	n/a	n/a
40	CTCF	chr2:55241180-55241330	HPAF	blood vessel:	n/a	n/a
41	RAD21	chr2:55241054-55241373	ECC-1	luminal epithelium:	n/a	n/a
42	RAD21	chr2:55241009-55241488	MCF-7	breast:	n/a	n/a
43	CTCF	chr2:55241080-55241230	HMF	breast:	n/a	n/a
44	RAD21	chr2:55241104-55241493	MCF-7	breast:	n/a	n/a
45	CTCF	chr2:55241200-55241350	HL-60	blood:	n/a	n/a
46	CTCF	chr2:55241120-55241434	K562	blood:	n/a	n/a
47	CTCF	chr2:55241012-55241503	HCT-116	colon:	n/a	n/a
48	IRF1	chr2:55241072-55241266	K562	blood:	n/a	chr2:55241214-55241226
49	STAT3	chr2:55241003-55241387	MCF10A-Er-Src	breast:	n/a	n/a
50	RAD21	chr2:55240985-55241535	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55240957..55243233-chr2:55273939..55276356,2	K562	blood:
2	chr2:55241176..55242945-chr2:55276344..55278140,2	MCF-7	breast:
3	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:

No data

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10210840	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11674808	0.83[EUR][1000 genomes]
rs12464070	0.89[ASN][1000 genomes]
rs12477711	0.92[ASN][1000 genomes]
rs12713284	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13011689	0.85[EUR][1000 genomes]
rs13387751	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2015919	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2044291	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255112	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2580764	0.82[ASN][1000 genomes]
rs2580765	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2580772	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2580773	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2580776	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2588510	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2588514	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2588517	0.92[ASN][1000 genomes]
rs2588518	0.95[ASN][1000 genomes]
rs2588521	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2860453	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2902649	0.92[ASN][1000 genomes]
rs2919129	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920878	0.80[EUR][1000 genomes]
rs2920893	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920900	0.83[EUR][1000 genomes]
rs2968786	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968787	0.88[ASN][1000 genomes]
rs2968790	0.84[EUR][1000 genomes]
rs2968793	0.85[EUR][1000 genomes]
rs2968794	0.82[EUR][1000 genomes]
rs2968795	0.85[EUR][1000 genomes]
rs2972072	0.83[EUR][1000 genomes]
rs2972075	0.84[EUR][1000 genomes]
rs2972090	0.85[ASN][1000 genomes]
rs2972097	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35631428	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35826668	0.94[ASN][1000 genomes]
rs3806570	0.96[ASN][1000 genomes]
rs4672005	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545466	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726158	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6755468	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760429	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7340476	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7562292	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7570629	0.84[AMR][1000 genomes]
rs7584430	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968998	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10174838	RTN4	cis	Thyroid	GTEx
rs10174838	RTN4	cis	Artery Tibial	GTEx
rs10174838	RTN4	cis	Whole Blood	GTEx
rs10174838	RTN4	cis	Nerve Tibial	GTEx
rs10174838	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs10174838	RTN4	cis	Esophagus Mucosa	GTEx
rs10174838	RTN4	cis	Artery Aorta	GTEx
rs10174838	RTN4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55236600-55241400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:55237200-55241600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
10	chr2:55237600-55241400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:55237600-55241400	Enhancers	Fetal Lung	lung
12	chr2:55237600-55241600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:55237600-55242000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
17	chr2:55237600-55249600	Weak transcription	Gastric	stomach
18	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:55237600-55258600	Weak transcription	Ovary	ovary
20	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
21	chr2:55237800-55241600	Enhancers	Duodenum Mucosa	Duodenum
22	chr2:55237800-55242200	Enhancers	NHLF	lung
23	chr2:55237800-55242800	Enhancers	Brain Substantia Nigra	brain
24	chr2:55237800-55242800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr2:55237800-55242800	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:55237800-55243000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:55237800-55243400	Enhancers	Osteobl	bone
28	chr2:55237800-55243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:55237800-55243600	Enhancers	Brain Hippocampus Middle	brain
30	chr2:55238000-55241400	Enhancers	Primary T cells from cord blood	blood
31	chr2:55238000-55241400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr2:55238000-55243000	Enhancers	Adipose Nuclei	Adipose
33	chr2:55238200-55245800	Weak transcription	Brain Germinal Matrix	brain
34	chr2:55238400-55241600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:55238400-55241600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:55238400-55242400	Enhancers	Liver	Liver
37	chr2:55238400-55242600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:55238400-55244600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:55238400-55249200	Weak transcription	Pancreas	Pancrea
40	chr2:55238400-55249600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:55238400-55250800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:55238400-55251200	Weak transcription	Psoas Muscle	Psoas
43	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
44	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
45	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:55239000-55241800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr2:55239200-55243000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr2:55239200-55244600	Weak transcription	Primary B cells from cord blood	blood
49	chr2:55239200-55244800	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:55239200-55247800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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