Variant report

Variant	rs4651024
Chromosome Location	chr1:179312102-179312103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179311628..179313681-chr1:179315946..179318351,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10913728	0.83[JPT][hapmap]
rs10913736	0.89[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs11577489	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11581507	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11799784	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11804236	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13306727	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13306730	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16853998	0.91[JPT][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17369088	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2152320	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184575	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs45471092	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4652366	0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs55906130	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs55986478	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56149964	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56303406	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57864135	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6425534	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6666358	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs6666455	0.91[GIH][hapmap]
rs6673354	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6682068	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67545145	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68098532	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534976	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4651024	TDRD5	cis	Artery Aorta	GTEx
rs4651024	FAM20B	cis	parietal	SCAN
rs4651024	TDRD5	cis	Nerve Tibial	GTEx
rs4651024	AXDND1	cis	Nerve Tibial	GTEx
rs4651024	SASS6	trans	parietal	SCAN
rs4651024	TDRD5	cis	Adipose Subcutaneous	GTEx
rs4651024	TDRD5	cis	Thyroid	GTEx
rs4651024	TDRD5	cis	Artery Tibial	GTEx
rs4651024	TDRD5	cis	cerebellum	SCAN
rs4651024	TDRD5	cis	parietal	SCAN
rs4651024	AXDND1	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
5	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
7	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
8	chr1:179280400-179314000	Weak transcription	NHLF	lung
9	chr1:179282000-179313000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:179282400-179313800	Weak transcription	HSMMtube	muscle
11	chr1:179286400-179313800	Weak transcription	Psoas Muscle	Psoas
12	chr1:179290800-179314000	Weak transcription	NHEK	skin
13	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:179293000-179322600	Weak transcription	Fetal Heart	heart
15	chr1:179293600-179313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:179293800-179314000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:179294200-179324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:179295600-179314000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:179296800-179327800	Weak transcription	Colonic Mucosa	Colon
20	chr1:179297400-179313600	Weak transcription	Spleen	Spleen
21	chr1:179297400-179321600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:179298600-179324200	Weak transcription	Thymus	Thymus
23	chr1:179299400-179316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:179299600-179312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:179300200-179313800	Weak transcription	Primary B cells from cord blood	blood
26	chr1:179300200-179314800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:179300600-179322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:179301800-179322800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:179303000-179314000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:179303200-179324600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:179303400-179322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:179303600-179314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:179304000-179313800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:179304200-179316000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:179304200-179316600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:179304200-179320000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:179304200-179324400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:179304200-179324400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:179304200-179324600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:179304200-179325200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:179304400-179318400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:179304400-179324400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:179304600-179316000	Strong transcription	Hela-S3	cervix
45	chr1:179304600-179324200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:179305200-179315800	Weak transcription	Brain Germinal Matrix	brain
47	chr1:179305200-179327200	Weak transcription	Right Ventricle	heart
48	chr1:179305400-179312400	Weak transcription	Fetal Intestine Small	intestine
49	chr1:179305600-179313600	Weak transcription	Lung	lung
50	chr1:179305600-179334200	Weak transcription	Pancreas	Pancrea

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