Variant report

Variant	rs4150407
Chromosome Location	chr2:128049631-128049632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:128049602-128049652	SK-N-MC	brain:	n/a
2	chr2:128049602-128049652	ECC-1	luminal epithelium:	n/a
3	chr2:128049602-128049652	Caco-2	colon:	n/a
4	chr2:128049602-128049652	NHBE	bronchial:	n/a
5	chr2:128049602-128049652	CMK	blood:	n/a
6	chr2:128049602-128049652	HRE	kidney:	n/a
7	chr2:128049602-128049652	SKMC	muscle:	n/a
8	chr2:128049602-128049652	GM06990	blood:	n/a
9	chr2:128049602-128049652	AG09309	skin:	n/a
10	chr2:128049602-128049652	PANC-1	pancreas:	n/a
11	chr2:128049602-128049652	HIPEpiC	eye:	n/a
12	chr2:128049602-128049652	GM12878	blood:	n/a
13	chr2:128049602-128049652	AG04450	lung:	fetal
14	chr2:128049602-128049652	BE2_C	brain:	n/a
15	chr2:128049602-128049652	SK-N-SH	brain:	n/a
16	chr2:128049602-128049652	HNPCEpiC	eye:	n/a
17	chr2:128049602-128049652	H1-hESC	embryonic stem cell:	embryo
18	chr2:128049602-128049652	A549	lung:	n/a
19	chr2:128049602-128049652	ovcar-3	ovarian:	n/a
20	chr2:128049602-128049652	HPAEpiC	pulmonary alveolar:	n/a
21	chr2:128049602-128049652	HCM	heart:	n/a
22	chr2:128049602-128049652	HEK293	kidney:	embryo
23	chr2:128049602-128049652	NH-A	brain:	n/a
24	chr2:128049602-128049652	ProgFib	skin:	n/a
25	chr2:128049602-128049652	T-47D	breast:	n/a
26	chr2:128049602-128049652	NT2-D1	testis:	n/a
27	chr2:128049602-128049652	AoSMC	blood vessel:	n/a
28	chr2:128049602-128049652	Hepatocyte	liver:	n/a
29	chr2:128049602-128049652	SAEC	small airway:	n/a
30	chr2:128049602-128049652	U87	brain:	n/a
31	chr2:128049602-128049652	HCPEpiC	choroid plexus:	n/a
32	chr2:128049602-128049652	PrEC	prostate:	n/a
33	chr2:128049602-128049652	GM19239	blood:	n/a
34	chr2:128049602-128049652	NB4	blood:	n/a
35	chr2:128049602-128049652	GM12892	blood:	n/a
36	chr2:128049602-128049652	NHDF-neo	bronchial:	n/a
37	chr2:128049602-128049652	SK-N-SH_RA	brain:	n/a
38	chr2:128049602-128049652	HRCEpiC	kidney:	n/a
39	chr2:128049602-128049652	AG09319	gingival:	n/a
40	chr2:128049602-128049652	PFSK-1	brain:	n/a
41	chr2:128049602-128049652	GM12891	blood:	n/a
42	chr2:128049602-128049652	HEEpiC	esophagus:	n/a
43	chr2:128049602-128049652	AG10803	skin:	n/a
44	chr2:128049602-128049652	HL-60	blood:	n/a
45	chr2:128049602-128049652	RPTEC	kidney:	n/a
46	chr2:128049602-128049652	HUVEC	blood vessel:	n/a
47	chr2:128049602-128049652	HAEpiC	amniotic membrane:	n/a
48	chr2:128049602-128049652	HCF	heart:	n/a
49	chr2:128049602-128049652	HRPEpiC	eye:	n/a
50	chr2:128049602-128049652	HCT-116	colon:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128045827..128047881-chr2:128049026..128051803,2	MCF-7	breast:
2	chr2:128047217..128049031-chr2:128049443..128051921,3	MCF-7	breast:

No data

Variant related genes	Relation type
ERCC3	CpG island
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10209678	0.91[ASN][1000 genomes]
rs10803585	0.90[ASN][1000 genomes]
rs10928761	0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11886231	0.97[ASN][1000 genomes]
rs11890187	0.95[ASN][1000 genomes]
rs11901355	0.84[ASN][1000 genomes]
rs12052483	0.89[ASN][1000 genomes]
rs12463451	0.98[ASN][1000 genomes]
rs12463909	0.89[EUR][1000 genomes]
rs12465955	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12469035	0.85[EUR][1000 genomes]
rs12477214	0.88[ASN][1000 genomes]
rs12479003	0.91[ASN][1000 genomes]
rs12622436	0.91[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs12623948	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12692064	0.91[ASN][1000 genomes]
rs12989081	0.89[ASN][1000 genomes]
rs12989154	0.91[ASN][1000 genomes]
rs12991062	0.83[ASN][1000 genomes]
rs12991768	0.86[ASN][1000 genomes]
rs13029237	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1566822	0.91[EUR][1000 genomes]
rs1566823	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs17015199	0.95[ASN][1000 genomes]
rs1850689	0.89[ASN][1000 genomes]
rs2090574	0.90[ASN][1000 genomes]
rs2174270	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2896888	0.85[EUR][1000 genomes]
rs2896980	0.89[ASN][1000 genomes]
rs34832797	0.91[ASN][1000 genomes]
rs35293119	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35328149	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3902960	0.92[EUR][1000 genomes]
rs4150441	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4150454	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4150477	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs4150495	0.97[ASN][1000 genomes]
rs4150496	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs4233583	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4233584	0.98[ASN][1000 genomes]
rs4497825	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4560059	0.89[EUR][1000 genomes]
rs4580338	0.87[EUR][1000 genomes]
rs4662575	0.96[ASN][1000 genomes]
rs4662578	0.95[ASN][1000 genomes]
rs4662580	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs4662710	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4662711	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4662712	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4662717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4662722	0.85[CEU][hapmap];0.94[ASN][1000 genomes]
rs4662725	0.89[ASN][1000 genomes]
rs55905117	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55998967	1.00[ASN][1000 genomes]
rs58475809	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59566504	0.91[ASN][1000 genomes]
rs62157549	0.95[ASN][1000 genomes]
rs62157555	0.94[ASN][1000 genomes]
rs62160261	0.82[ASN][1000 genomes]
rs6430931	0.84[EUR][1000 genomes]
rs6430935	0.93[ASN][1000 genomes]
rs6712213	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6712446	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6712551	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6731176	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6732279	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6761447	0.95[ASN][1000 genomes]
rs71414745	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7568261	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7580658	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs7585198	0.80[EUR][1000 genomes]
rs7589451	0.90[ASN][1000 genomes]
rs7591760	0.82[EUR][1000 genomes]
rs867304	0.95[ASN][1000 genomes]
rs9636235	0.91[EUR][1000 genomes]
rs9636236	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs9636237	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.95[ASN][1000 genomes]
rs9789510	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[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	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4150407	ERCC3	cis	cerebellum	SCAN
rs4150407	ERCC3	cis	parietal	SCAN
rs4150407	TUBA3E	cis	parietal	SCAN
rs4150407	MAP3K2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128021200-128050000	Strong transcription	Fetal Stomach	stomach
2	chr2:128023400-128050400	Strong transcription	Liver	Liver
3	chr2:128024200-128050600	Strong transcription	Fetal Intestine Large	intestine
4	chr2:128024400-128049800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:128024400-128050000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:128024400-128050200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:128024400-128050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:128024400-128050200	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:128024400-128050400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:128024400-128050400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:128024400-128050400	Strong transcription	Thymus	Thymus
12	chr2:128024400-128050800	Strong transcription	Fetal Thymus	thymus
13	chr2:128024600-128050000	Strong transcription	HepG2	liver
14	chr2:128024600-128050200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:128024600-128050200	Strong transcription	Adipose Nuclei	Adipose
16	chr2:128024800-128050000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:128024800-128050200	Strong transcription	Brain Anterior Caudate	brain
18	chr2:128024800-128050200	Strong transcription	Brain Hippocampus Middle	brain
19	chr2:128024800-128050200	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:128024800-128050200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr2:128024800-128050400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr2:128024800-128050400	Strong transcription	Osteobl	bone
23	chr2:128025000-128050600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:128025200-128050000	Strong transcription	Left Ventricle	heart
25	chr2:128025200-128050200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:128025800-128050000	Strong transcription	Spleen	Spleen
27	chr2:128033800-128050400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:128034200-128050200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:128034200-128050200	Strong transcription	K562	blood
30	chr2:128034400-128050000	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr2:128034400-128050200	Strong transcription	HUVEC	blood vessel
32	chr2:128034800-128050400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:128036600-128050200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:128036600-128050800	Weak transcription	Right Atrium	heart
35	chr2:128036800-128050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:128037400-128050400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:128037400-128050400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:128037400-128050600	Strong transcription	Right Ventricle	heart
39	chr2:128039200-128050000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:128039200-128050200	Strong transcription	Brain Substantia Nigra	brain
41	chr2:128039200-128050400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:128039200-128050400	Strong transcription	Ovary	ovary
43	chr2:128039200-128050600	Strong transcription	NHEK	skin
44	chr2:128039400-128050200	Strong transcription	Placenta	Placenta
45	chr2:128039800-128050000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:128039800-128050400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:128039800-128050400	Strong transcription	Fetal Kidney	kidney
48	chr2:128040000-128050000	Strong transcription	Pancreas	Pancrea
49	chr2:128040200-128050000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr2:128040200-128050400	Strong transcription	Muscle Satellite Cultured Cells	--

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