Variant report

Variant	rs2581780
Chromosome Location	chr3:53058960-53058961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53047316..53051698-chr3:53056732..53062167,5	MCF-7	breast:
2	chr3:53058305..53064318-chr3:53075790..53081540,9	K562	blood:
3	chr3:53058305..53060040-chr3:53077970..53080050,2	K562	blood:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11130332	0.93[EUR][1000 genomes]
rs1134546	1.00[CEU][hapmap]
rs11707576	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11708223	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13082061	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13083728	0.82[CEU][hapmap]
rs1573815	0.82[CEU][hapmap]
rs17304995	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2245424	0.87[JPT][hapmap]
rs2246556	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2255107	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2257216	0.86[JPT][hapmap]
rs2276817	0.82[CEU][hapmap]
rs2276825	0.94[CEU][hapmap]
rs2336162	0.85[EUR][1000 genomes]
rs2336669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2336670	0.85[JPT][hapmap]
rs2336671	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581779	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581796	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581797	0.93[EUR][1000 genomes]
rs2581801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581802	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581803	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2581805	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]
rs2581820	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2581823	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710314	0.87[JPT][hapmap]
rs2710345	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34230854	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35380116	0.91[EUR][1000 genomes]
rs3733047	0.82[CEU][hapmap]
rs4302374	0.94[CEU][hapmap]
rs4519686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687554	0.82[CEU][hapmap]
rs4687692	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687699	0.83[EUR][1000 genomes]
rs59989280	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6445538	0.82[CEU][hapmap]
rs6445539	0.82[CEU][hapmap]
rs6445547	0.94[CEU][hapmap]
rs6445550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770957	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6771610	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6789219	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6792578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6803519	0.82[CEU][hapmap]
rs6805298	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71301803	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71301807	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621939	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637082	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644973	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7648514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7652131	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs9682464	0.88[CEU][hapmap]
rs9812543	0.94[EUR][1000 genomes]
rs9813024	0.90[EUR][1000 genomes]
rs9823697	0.86[JPT][hapmap]
rs9828491	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9831409	0.93[EUR][1000 genomes]
rs9842974	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9844736	1.00[CEU][hapmap]
rs9846976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9847024	0.87[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9876403	0.94[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876799	chr3:53024216-53060637	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv590321	chr3:53027983-53062661	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2581780	ITIH4-AS1	cis	lung	GTEx
rs2581780	SERBP1P3	cis	lung	GTEx
rs2581780	PPM1M	cis	Artery Tibial	GTEx
rs2581780	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2581780	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs2581780	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2581780	MUSTN1	cis	Artery Aorta	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53025600-53061600	Weak transcription	Lung	lung
2	chr3:53027600-53061600	Weak transcription	Liver	Liver
3	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
5	chr3:53033800-53060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:53033800-53065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:53037000-53065000	Weak transcription	Fetal Intestine Small	intestine
8	chr3:53040800-53065000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:53043800-53064800	Weak transcription	Stomach Mucosa	stomach
10	chr3:53044600-53065000	Weak transcription	Gastric	stomach
11	chr3:53045200-53061400	Weak transcription	Fetal Heart	heart
12	chr3:53045400-53061600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:53045800-53061400	Weak transcription	HepG2	liver
14	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:53049200-53059800	Weak transcription	Pancreas	Pancrea
16	chr3:53050600-53062000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:53052000-53064800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:53053000-53063600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:53053800-53061600	Weak transcription	Ovary	ovary
20	chr3:53054000-53070600	Weak transcription	Right Ventricle	heart
21	chr3:53054400-53059800	Weak transcription	Primary B cells from cord blood	blood
22	chr3:53054400-53064800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:53055600-53060800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:53056200-53059600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:53056600-53065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:53056600-53077800	Weak transcription	Fetal Stomach	stomach
27	chr3:53057000-53060000	Enhancers	Dnd41	blood
28	chr3:53057400-53065000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:53057600-53059800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:53057600-53061400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:53057800-53060400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:53057800-53063600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:53057800-53063600	Weak transcription	Primary T cells from cord blood	blood
34	chr3:53057800-53063600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:53057800-53063800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:53057800-53064600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:53058000-53059800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:53058000-53059800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:53058000-53060400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:53058000-53060600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:53058000-53061200	Weak transcription	HUVEC	blood vessel
42	chr3:53058000-53062800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:53058200-53059000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr3:53058200-53059800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:53058200-53061600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:53058400-53061200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:53058600-53059600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:53058600-53060000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:53058600-53060600	Weak transcription	Left Ventricle	heart
50	chr3:53058600-53060800	Weak transcription	Psoas Muscle	Psoas

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