Variant report

Variant	rs56149964
Chromosome Location	chr1:179326065-179326066
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179324764..179330437-chr1:179332106..179336685,6	K562	blood:
2	chr1:179319218..179322738-chr1:179324103..179326545,3	K562	blood:
3	chr1:179325938..179328666-chr1:179330165..179332477,2	K562	blood:
4	chr1:179317813..179320620-chr1:179325439..179328200,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162779	Chromatin interaction
ENSG00000263633	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10913736	0.81[ASN][1000 genomes]
rs11577489	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11581507	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11799784	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11804236	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13306727	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13306730	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16853998	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16854003	0.81[ASN][1000 genomes]
rs17369088	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2152320	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184575	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45471092	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651024	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652366	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55906130	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55986478	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56303406	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57864135	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6425534	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666358	0.84[ASN][1000 genomes]
rs6673354	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6682068	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67545145	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68098532	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525946	0.81[EUR][1000 genomes]
rs7534976	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv1804302	chr1:179315357-179333194	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv548277	chr1:179319868-179333194	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1809332	chr1:179320578-179333194	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv548278	chr1:179323919-179333194	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56149964	AXDND1	cis	Thyroid	GTEx
rs56149964	SOAT1	cis	Whole Blood	GTEx
rs56149964	TDRD5	cis	Thyroid	GTEx
rs56149964	TDRD5	cis	Nerve Tibial	GTEx
rs56149964	TDRD5	cis	Adipose Subcutaneous	GTEx
rs56149964	AXDND1	cis	Nerve Tibial	GTEx
rs56149964	TDRD5	cis	Artery Aorta	GTEx
rs56149964	TDRD5	cis	Esophagus Mucosa	GTEx
rs56149964	TDRD5	cis	Artery Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:179296800-179327800	Weak transcription	Colonic Mucosa	Colon
4	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:179305200-179327200	Weak transcription	Right Ventricle	heart
6	chr1:179305600-179334200	Weak transcription	Pancreas	Pancrea
7	chr1:179309800-179326400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:179311600-179326400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:179312600-179334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:179314600-179326200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:179314800-179327800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:179314800-179334400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:179315000-179334400	Weak transcription	Brain Substantia Nigra	brain
14	chr1:179315000-179334400	Weak transcription	Left Ventricle	heart
15	chr1:179315400-179334400	Weak transcription	Fetal Kidney	kidney
16	chr1:179315600-179334400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:179315800-179334200	Weak transcription	Fetal Thymus	thymus
18	chr1:179316000-179327600	Weak transcription	Brain Angular Gyrus	brain
19	chr1:179316000-179334000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:179316000-179334200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:179316000-179334400	Weak transcription	Fetal Brain Female	brain
22	chr1:179316000-179334400	Weak transcription	Ovary	ovary
23	chr1:179316400-179332800	Weak transcription	Fetal Intestine Small	intestine
24	chr1:179317600-179334400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:179317800-179327800	Weak transcription	NHEK	skin
26	chr1:179319200-179334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:179319800-179334000	Weak transcription	HepG2	liver
28	chr1:179319800-179334200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:179320000-179334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:179320600-179327200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:179320800-179334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:179320800-179334200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:179320800-179334400	Weak transcription	Fetal Lung	lung
34	chr1:179321000-179334200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:179321200-179334400	Weak transcription	Fetal Stomach	stomach
36	chr1:179321200-179334400	Weak transcription	Lung	lung
37	chr1:179321600-179327600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:179321800-179327200	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:179322000-179327200	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:179322400-179334200	Weak transcription	Primary B cells from cord blood	blood
41	chr1:179323000-179330600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:179323000-179333400	Weak transcription	Placenta	Placenta
43	chr1:179323000-179334200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:179323000-179334200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:179323000-179334200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:179323000-179334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:179323000-179334400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:179323000-179334400	Weak transcription	NH-A	brain
49	chr1:179323000-179334400	Weak transcription	Osteobl	bone
50	chr1:179323200-179330200	Weak transcription	Brain Anterior Caudate	brain

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