Variant report

Variant	rs2329020
Chromosome Location	chr3:49685073-49685074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49576104..49578514-chr3:49684857..49687792,2	MCF-7	breast:
2	chr3:49683730..49686310-chr3:49694623..49697344,2	K562	blood:
3	chr3:49676360..49678118-chr3:49683625..49686002,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1050088	0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap]
rs1060962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865955	0.86[ASW][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap]
rs11130199	0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs11130212	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130213	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs1131095	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11709525	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11710037	0.92[ASN][1000 genomes]
rs11711485	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs11718165	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs11720264	0.86[JPT][hapmap];0.83[YRI][hapmap]
rs11917431	0.87[ASN][1000 genomes]
rs11919311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11921590	0.87[ASN][1000 genomes]
rs12489092	0.86[JPT][hapmap]
rs12490267	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12497288	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12636099	0.80[AFR][1000 genomes]
rs13085791	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13316695	0.92[ASN][1000 genomes]
rs1352890	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1568661	0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap]
rs1801143	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs1826347	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap]
rs1873625	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1873626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005557	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2131104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2131109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2172252	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2960548	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3197999	0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34762726	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35007338	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35404120	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35701831	0.94[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs3811697	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs3870338	0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs3924462	0.86[ASW][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.84[YRI][hapmap]
rs4283605	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4625	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4855835	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855839	0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4855847	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855859	0.86[ASW][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs4855864	0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4855881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855883	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855884	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6765869	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6766131	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs6767878	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6770670	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6782577	0.96[CEU][hapmap]
rs6803222	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7614725	0.87[ASN][1000 genomes]
rs7622302	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs7633271	0.86[JPT][hapmap]
rs7637999	0.86[ASW][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.84[YRI][hapmap]
rs885592	0.86[ASW][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.84[YRI][hapmap]
rs9812791	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9822268	0.92[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9823546	0.81[ASN][1000 genomes]
rs9824092	0.92[ASN][1000 genomes]
rs9827021	0.86[JPT][hapmap]
rs9827708	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9833611	0.87[ASN][1000 genomes]
rs9836291	0.81[ASN][1000 genomes]
rs9837027	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9837341	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9837520	0.87[ASN][1000 genomes]
rs9841110	0.86[JPT][hapmap]
rs9853683	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9858280	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9858542	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs9862080	0.92[ASN][1000 genomes]
rs9875617	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9882740	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2329020	ALS2CL	cis	cerebellum	SCAN
rs2329020	WDR6	cis	multi-tissue	Pritchard
rs2329020	CISH	cis	lymphoblastoid	seeQTL
rs2329020	IP6K2	cis	cerebellum	SCAN
rs2329020	WDR6	cis	lymphoblastoid	seeQTL
rs2329020	CCDC71	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:49661600-49692400	Weak transcription	Ovary	ovary
3	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:49673800-49692400	Weak transcription	Gastric	stomach
5	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:49676000-49686400	Weak transcription	Spleen	Spleen
7	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
8	chr3:49676400-49687000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:49679600-49687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr3:49681000-49685400	Weak transcription	Fetal Stomach	stomach
12	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:49682000-49685200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:49682600-49688400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:49683000-49687000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:49683200-49685200	Weak transcription	Brain Germinal Matrix	brain
19	chr3:49683200-49686000	Enhancers	Brain Angular Gyrus	brain
20	chr3:49683200-49686600	Enhancers	Pancreas	Pancrea
21	chr3:49684400-49685800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:49684600-49685600	Enhancers	Primary hematopoietic stem cells	blood
23	chr3:49684600-49686000	Enhancers	Adipose Nuclei	Adipose
24	chr3:49684600-49686000	Enhancers	Brain Anterior Caudate	brain
25	chr3:49684600-49686600	Enhancers	Right Atrium	heart
26	chr3:49684600-49687400	Enhancers	Fetal Heart	heart
27	chr3:49684600-49687800	Genic enhancers	Brain Inferior Temporal Lobe	brain
28	chr3:49684800-49685800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:49684800-49686000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:49684800-49687400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:49684800-49687400	Enhancers	Left Ventricle	heart
32	chr3:49684800-49687600	Enhancers	Psoas Muscle	Psoas
33	chr3:49684800-49688000	Enhancers	HepG2	liver
34	chr3:49684800-49688400	Enhancers	Fetal Muscle Leg	muscle
35	chr3:49684800-49688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:49684800-49689400	Enhancers	Fetal Muscle Trunk	muscle
37	chr3:49685000-49685400	Genic enhancers	Fetal Brain Female	brain
38	chr3:49685000-49685400	Enhancers	Lung	lung
39	chr3:49685000-49685400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:49685000-49685600	Enhancers	Liver	Liver
41	chr3:49685000-49686000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:49685000-49686000	Enhancers	Hela-S3	cervix
43	chr3:49685000-49686200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:49685000-49686200	Enhancers	Fetal Lung	lung
45	chr3:49685000-49686600	Enhancers	Right Ventricle	heart
46	chr3:49685000-49687400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:49685000-49687600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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