Variant report

Variant	rs11579176
Chromosome Location	chr1:46050561-46050562
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:47)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45671368..45673196-chr1:46049777..46051342,2	K562	blood:
2	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
3	chr1:46047808..46051262-chr1:46767344..46769900,3	K562	blood:
4	chr1:46048444..46052841-chr10:129795145..129798145,4	K562	blood:
5	chr1:45185636..45188407-chr1:46047872..46052515,5	K562	blood:
6	chr1:45973068..45975148-chr1:46049390..46051110,2	MCF-7	breast:
7	chr1:46047578..46050794-chr1:46077080..46080053,4	K562	blood:
8	chr1:45987123..45987876-chr1:46049809..46050706,2	Hela-S3	cervix:
9	chr1:45283391..45288738-chr1:46048072..46051277,6	K562	blood:
10	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
11	chr1:45194369..45197773-chr1:46046767..46051199,5	K562	blood:
12	chr1:46049223..46051857-chr1:46080346..46084237,3	K562	blood:
13	chr1:45986151..45989227-chr1:46047437..46050636,3	MCF-7	breast:
14	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
15	chr1:45803780..45809046-chr1:46047811..46052394,14	K562	blood:
16	chr1:46014878..46016600-chr1:46048610..46051417,2	MCF-7	breast:
17	chr1:45974971..45980027-chr1:46048272..46053531,9	K562	blood:
18	chr1:46049190..46051065-chr1:46268579..46270111,2	K562	blood:
19	chr1:46026984..46033199-chr1:46047562..46051151,12	K562	blood:
20	chr1:45271675..45274360-chr1:46048607..46050864,2	K562	blood:
21	chr1:46048446..46052403-chr1:46150752..46155740,15	K562	blood:
22	chr1:46050490..46052204-chr1:46662949..46664984,2	K562	blood:
23	chr1:46049211..46052214-chr1:46711116..46714432,3	K562	blood:
24	chr1:46015193..46018509-chr1:46048657..46051369,3	MCF-7	breast:
25	chr1:46049133..46051352-chr1:46267497..46269310,2	MCF-7	breast:
26	chr1:45186130..45188407-chr1:46047872..46051720,5	K562	blood:
27	chr1:46048335..46051372-chr1:46110517..46113642,3	K562	blood:
28	chr1:45477030..45479805-chr1:46047527..46050763,5	K562	blood:
29	chr1:46049506..46051127-chr1:46805584..46807919,2	K562	blood:
30	chr1:46049686..46051215-chr10:129795123..129796643,2	MCF-7	breast:
31	chr1:46034190..46037574-chr1:46047982..46052662,9	K562	blood:
32	chr1:46048069..46054740-chr1:46150080..46155979,19	K562	blood:
33	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
34	chr1:45195288..45198728-chr1:46046767..46051124,6	K562	blood:
35	chr1:46049909..46050833-chr16:67208150..67208708,2	Hela-S3	cervix:
36	chr1:45951915..45956979-chr1:46048471..46052743,8	K562	blood:
37	chr1:11968732..11970324-chr1:46049073..46051914,2	K562	blood:
38	chr1:46012228..46018632-chr1:46046407..46053601,17	K562	blood:
39	chr1:45960198..45962227-chr1:46049813..46051584,2	K562	blood:
40	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
41	chr1:45284255..45286941-chr1:46048411..46051884,4	K562	blood:
42	chr1:46049275..46051699-chr1:46215070..46217798,3	K562	blood:
43	chr1:45985173..45987673-chr1:46047489..46052049,5	MCF-7	breast:
44	chr1:46032390..46034451-chr1:46048805..46051197,3	MCF-7	breast:
45	chr1:45240022..45242115-chr1:46048297..46050844,3	K562	blood:
46	chr1:45803780..45808811-chr1:46047553..46051220,11	K562	blood:
47	chr1:45264331..45266422-chr1:46049131..46050804,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197429	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000086015	Chromatin interaction
ENSG00000117481	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000225447	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000132334	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1053941	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11582058	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11585275	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11587982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11590549	0.95[CEU][hapmap]
rs12042481	1.00[ASW][hapmap]
rs2065708	0.81[GIH][hapmap]
rs28433203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs28584711	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs3014232	1.00[ASN][1000 genomes]
rs41310432	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs532639	1.00[ASN][1000 genomes]
rs534534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55951835	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56020747	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067046	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56238114	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56261438	1.00[ASN][1000 genomes]
rs58692133	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429573	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6662572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs6662999	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6671239	0.83[AMR][1000 genomes]
rs72688452	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72688460	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7517111	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7553374	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11579176	CCDC163P	cis	Heart Left Ventricle	GTEx
rs11579176	CCDC163P	cis	Esophagus Mucosa	GTEx
rs11579176	CCDC163P	cis	Thyroid	GTEx
rs11579176	CCDC163P	cis	Nerve Tibial	GTEx
rs11579176	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs11579176	MED8	cis	cerebellum	SCAN
rs11579176	CCDC163P	cis	Whole Blood	GTEx
rs11579176	CCDC163P	cis	Stomach	GTEx
rs11579176	CCDC163P	cis	lung	GTEx
rs11579176	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs11579176	CCDC163P	cis	Muscle Skeletal	GTEx
rs11579176	CCDC163P	cis	Artery Tibial	GTEx
rs11579176	CCDC163P	cis	Esophagus Muscularis	GTEx
rs11579176	CCDC163P	cis	Artery Aorta	GTEx
rs11579176	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46048600-46051000	Active TSS	Colonic Mucosa	Colon
2	chr1:46048800-46050600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:46048800-46050600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:46048800-46050600	Active TSS	Brain Anterior Caudate	brain
5	chr1:46048800-46050600	Active TSS	Brain Cingulate Gyrus	brain
6	chr1:46048800-46050600	Active TSS	Left Ventricle	heart
7	chr1:46048800-46050600	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr1:46048800-46050600	Active TSS	NHEK	skin
9	chr1:46048800-46050800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:46048800-46050800	Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:46048800-46050800	Active TSS	Brain Germinal Matrix	brain
12	chr1:46048800-46050800	Active TSS	Brain Hippocampus Middle	brain
13	chr1:46048800-46050800	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr1:46048800-46050800	Active TSS	Fetal Brain Female	brain
15	chr1:46048800-46050800	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:46048800-46050800	Active TSS	HSMMtube	muscle
17	chr1:46048800-46050800	Active TSS	K562	blood
18	chr1:46048800-46050800	Active TSS	NH-A	brain
19	chr1:46048800-46051000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:46048800-46051000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:46048800-46051000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:46048800-46051000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:46048800-46051000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:46048800-46051000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:46048800-46051000	Active TSS	Fetal Stomach	stomach
26	chr1:46048800-46051000	Active TSS	Psoas Muscle	Psoas
27	chr1:46048800-46051000	Active TSS	Hela-S3	cervix
28	chr1:46048800-46051000	Active TSS	HSMM	muscle
29	chr1:46048800-46051000	Active TSS	NHLF	lung
30	chr1:46048800-46051200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:46048800-46051200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:46048800-46051200	Active TSS	Fetal Kidney	kidney
33	chr1:46048800-46051200	Active TSS	Right Ventricle	heart
34	chr1:46048800-46051200	Active TSS	NHDF-Ad	bronchial
35	chr1:46048800-46051400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:46048800-46051800	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr1:46048800-46051800	Active TSS	H1 Cell Line	embryonic stem cell
38	chr1:46048800-46052200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:46048800-46052200	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr1:46048800-46052400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:46048800-46052600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr1:46048800-46052600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr1:46048800-46052800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr1:46049000-46050600	Active TSS	Primary hematopoietic stem cells	blood
45	chr1:46049000-46050600	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr1:46049000-46050600	Active TSS	Adipose Nuclei	Adipose
47	chr1:46049000-46050600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr1:46049000-46050600	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr1:46049000-46050600	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:46049000-46050600	Active TSS	Stomach Smooth Muscle	stomach

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