Variant report

Variant	rs3753525
Chromosome Location	chr1:179311602-179311603
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1044925	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs10753193	0.83[CHD][hapmap]
rs10798666	0.89[ASN][1000 genomes]
rs12024173	0.91[ASN][1000 genomes]
rs12140800	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs2065761	0.81[ASN][1000 genomes]
rs2152319	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3753527	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs4360482	0.83[CHD][hapmap]
rs4606280	0.83[CHD][hapmap]
rs61821461	0.91[ASN][1000 genomes]
rs6425535	0.86[ASN][1000 genomes]
rs6659294	0.83[CHD][hapmap]
rs6662859	0.83[CHD][hapmap]
rs6675699	0.91[ASN][1000 genomes]
rs7349152	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7536854	0.91[ASN][1000 genomes]
rs7537139	0.91[ASN][1000 genomes]
rs7548288	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[ASN][1000 genomes]
rs7551027	0.91[ASN][1000 genomes]
rs7556547	0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3753525	TDRD5	cis	parietal	SCAN
rs3753525	RASAL2	cis	parietal	SCAN

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	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
8	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
9	chr1:179280400-179314000	Weak transcription	NHLF	lung
10	chr1:179282000-179313000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:179282400-179313800	Weak transcription	HSMMtube	muscle
12	chr1:179286400-179313800	Weak transcription	Psoas Muscle	Psoas
13	chr1:179290800-179314000	Weak transcription	NHEK	skin
14	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:179293000-179311800	Weak transcription	Fetal Kidney	kidney
16	chr1:179293000-179322600	Weak transcription	Fetal Heart	heart
17	chr1:179293600-179313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:179293800-179311800	Weak transcription	HMEC	breast
19	chr1:179293800-179314000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:179294200-179324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:179295600-179314000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:179296800-179327800	Weak transcription	Colonic Mucosa	Colon
23	chr1:179297400-179313600	Weak transcription	Spleen	Spleen
24	chr1:179297400-179321600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:179297800-179311800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:179298600-179324200	Weak transcription	Thymus	Thymus
27	chr1:179299400-179316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:179299600-179312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:179300200-179313800	Weak transcription	Primary B cells from cord blood	blood
30	chr1:179300200-179314800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:179300600-179322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:179301800-179322800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:179303000-179314000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:179303200-179324600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:179303400-179322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:179303600-179311800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:179303600-179314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:179304000-179313800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:179304200-179316000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:179304200-179316600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:179304200-179320000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:179304200-179324400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:179304200-179324400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:179304200-179324600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:179304200-179325200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:179304400-179318400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:179304400-179324400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:179304600-179316000	Strong transcription	Hela-S3	cervix
50	chr1:179304600-179324200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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