Variant report

Variant	rs2581779
Chromosome Location	chr3:53056199-53056200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53055176..53056730-chr3:53078490..53080404,2	MCF-7	breast:
2	chr3:53056126..53058134-chr3:53061359..53063994,2	K562	blood:
3	chr3:53054569..53056705-chr3:53106775..53108496,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11130332	0.93[EUR][1000 genomes]
rs11707576	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11708223	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13082061	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17304995	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2246556	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2255107	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2336162	0.85[EUR][1000 genomes]
rs2336669	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2336671	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2564947	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2581780	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581796	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581797	0.93[EUR][1000 genomes]
rs2581801	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581802	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581805	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581810	0.90[EUR][1000 genomes]
rs2581815	0.93[EUR][1000 genomes]
rs2581820	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581823	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2710345	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34230854	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35380116	0.91[EUR][1000 genomes]
rs4519686	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687692	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687699	0.83[EUR][1000 genomes]
rs59989280	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6445550	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768844	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770957	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771610	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6789219	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6792578	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6805298	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71301803	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71301807	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621939	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7637082	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644973	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7648514	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7652131	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311485	0.92[EUR][1000 genomes]
rs9812543	0.94[EUR][1000 genomes]
rs9813024	0.90[EUR][1000 genomes]
rs9828491	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9831409	0.93[EUR][1000 genomes]
rs9842974	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846976	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847024	0.87[EUR][1000 genomes]
rs9865094	0.92[EUR][1000 genomes]
rs9870898	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9876403	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2581779	ITIH4-AS1	cis	lung	GTEx
rs2581779	MUSTN1	cis	Artery Aorta	GTEx
rs2581779	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2581779	SERBP1P3	cis	lung	GTEx
rs2581779	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2581779	ITIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:53019600-53056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:53020600-53057000	Weak transcription	Dnd41	blood
4	chr3:53025600-53061600	Weak transcription	Lung	lung
5	chr3:53027600-53061600	Weak transcription	Liver	Liver
6	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
8	chr3:53033200-53057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:53033600-53056200	Weak transcription	Fetal Stomach	stomach
10	chr3:53033800-53060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:53033800-53065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:53037000-53065000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:53040800-53065000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:53043800-53064800	Weak transcription	Stomach Mucosa	stomach
15	chr3:53044600-53065000	Weak transcription	Gastric	stomach
16	chr3:53045200-53061400	Weak transcription	Fetal Heart	heart
17	chr3:53045400-53057200	Weak transcription	Psoas Muscle	Psoas
18	chr3:53045400-53061600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:53045600-53057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:53045600-53057600	Weak transcription	Left Ventricle	heart
21	chr3:53045800-53061400	Weak transcription	HepG2	liver
22	chr3:53046000-53057600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:53048400-53058600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:53049200-53059800	Weak transcription	Pancreas	Pancrea
26	chr3:53050600-53057200	Weak transcription	Small Intestine	intestine
27	chr3:53050600-53062000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:53051400-53056600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:53051800-53056800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:53052000-53064800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:53052800-53056600	Weak transcription	Primary T cells from cord blood	blood
32	chr3:53052800-53057000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:53053000-53057200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:53053000-53057400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:53053000-53057600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:53053000-53063600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:53053200-53056800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:53053200-53057000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:53053200-53057600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:53053400-53058200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:53053800-53061600	Weak transcription	Ovary	ovary
42	chr3:53054000-53070600	Weak transcription	Right Ventricle	heart
43	chr3:53054200-53056400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:53054200-53056600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:53054400-53059800	Weak transcription	Primary B cells from cord blood	blood
46	chr3:53054400-53064800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:53055600-53057200	Weak transcription	Brain Germinal Matrix	brain
48	chr3:53055600-53058400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr3:53055600-53060800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:53056000-53056200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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