Variant report

Variant	rs3770411
Chromosome Location	chr2:53913609-53913610
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10490465	0.84[AFR][1000 genomes]
rs10490468	0.84[CHB][hapmap];0.88[CHD][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs11897282	0.89[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs11901698	0.84[CEU][hapmap];0.92[CHB][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs13408029	0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs17045048	0.87[AFR][1000 genomes]
rs17045084	0.84[AFR][1000 genomes]
rs17045176	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs17045203	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs17520505	0.85[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs17521008	0.89[ASW][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs2287340	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs2302797	0.89[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs2542572	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2542573	0.80[ASN][1000 genomes]
rs2542581	0.89[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap]
rs2542582	0.85[CHB][hapmap]
rs2542589	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2542590	0.82[ASN][1000 genomes]
rs2542591	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2543629	0.81[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap]
rs2692519	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs2692522	0.80[ASN][1000 genomes]
rs2692533	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs2949813	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap]
rs35772199	0.93[ASN][1000 genomes]
rs3731970	0.89[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs3770394	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs3770395	0.86[ASN][1000 genomes]
rs3770397	0.84[ASN][1000 genomes]
rs3770399	0.86[ASN][1000 genomes]
rs3770407	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs3770408	0.92[AFR][1000 genomes]
rs3930	0.89[CEU][hapmap]
rs4116709	0.85[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs55897904	0.82[ASN][1000 genomes]
rs58125503	0.80[AFR][1000 genomes]
rs62137565	0.85[ASN][1000 genomes]
rs62137573	0.88[ASN][1000 genomes]
rs62137602	0.84[ASN][1000 genomes]
rs62137606	0.86[ASN][1000 genomes]
rs62139773	0.86[AFR][1000 genomes]
rs62139785	0.85[AFR][1000 genomes]
rs6730006	0.89[ASN][1000 genomes]
rs719127	0.84[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs72901209	0.92[AFR][1000 genomes]
rs72901256	0.88[ASN][1000 genomes]
rs73934971	0.85[AFR][1000 genomes]
rs7600817	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1009107	chr2:53896767-53946913	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014949	chr2:53896767-53947781	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1011400	chr2:53899956-53947781	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3770411	TSPYL6	cis	cerebellum	SCAN
rs3770411	PSME4	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:53888200-53934200	Weak transcription	Lung	lung
5	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
6	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
7	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:53892600-53918800	Weak transcription	Left Ventricle	heart
9	chr2:53893400-53915200	Weak transcription	Ovary	ovary
10	chr2:53893800-53926800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:53894200-53920800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:53894400-53914400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:53894400-53925000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:53895400-53919000	Weak transcription	Fetal Intestine Large	intestine
16	chr2:53895400-53921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:53895400-53925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:53895400-53926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:53895600-53914800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:53895600-53921400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:53895800-53916800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:53895800-53926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:53896000-53918800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:53896200-53918400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:53896400-53926000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:53896800-53918800	Weak transcription	Fetal Brain Female	brain
27	chr2:53896800-53924800	Weak transcription	Thymus	Thymus
28	chr2:53896800-53936600	Weak transcription	Aorta	Aorta
29	chr2:53898000-53914800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:53898000-53918800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:53898200-53919400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:53898200-53935400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:53898200-53935400	Weak transcription	Fetal Kidney	kidney
35	chr2:53898600-53914400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:53899600-53914600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:53900600-53915200	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:53900600-53915400	Weak transcription	HSMM	muscle
39	chr2:53900600-53921400	Weak transcription	Brain Angular Gyrus	brain
40	chr2:53900600-53926400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:53900600-53935600	Weak transcription	K562	blood
42	chr2:53900800-53918800	Weak transcription	Brain Substantia Nigra	brain
43	chr2:53900800-53936400	Weak transcription	NH-A	brain
44	chr2:53900800-53936800	Weak transcription	NHLF	lung
45	chr2:53903600-53918800	Weak transcription	Psoas Muscle	Psoas
46	chr2:53906600-53933800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:53906800-53935200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:53907200-53927000	Weak transcription	Placenta	Placenta
49	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
50	chr2:53908800-53926000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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