Variant report

Variant	rs2837257
Chromosome Location	chr21:41223196-41223197
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:41221313..41224011-chr21:41232632..41234576,2	MCF-7	breast:
2	chr21:41197122..41199779-chr21:41222569..41224970,2	MCF-7	breast:
3	chr21:41219658..41221739-chr21:41222573..41224525,2	MCF-7	breast:
4	chr21:41217185..41219061-chr21:41222120..41225163,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1004663	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1018352	0.81[JPT][hapmap]
rs10470190	0.81[JPT][hapmap]
rs11701338	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12626544	0.86[JPT][hapmap]
rs12627540	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1571712	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1984023	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2205205	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2244761	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837175	0.81[JPT][hapmap]
rs2837176	0.81[JPT][hapmap]
rs2837178	0.81[JPT][hapmap]
rs2837183	0.86[JPT][hapmap]
rs2837206	0.86[JPT][hapmap]
rs2837208	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2837214	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2837215	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2837218	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837219	0.82[ASN][1000 genomes]
rs2837221	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2837223	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837225	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837226	0.90[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837227	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837229	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2837232	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837246	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2837247	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837249	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837253	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837258	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837259	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837260	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4337554	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs461583	0.86[JPT][hapmap]
rs4816652	0.81[JPT][hapmap]
rs4816653	0.81[JPT][hapmap]
rs4818088	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4818092	0.86[JPT][hapmap]
rs4818094	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4818098	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7277375	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7278733	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs731592	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs741866	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs760285	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs760286	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9305680	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs981653	0.86[JPT][hapmap]
rs9974301	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9974413	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9978994	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9979170	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9979395	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9980807	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9980954	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9982214	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9982243	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9982859	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1065086	chr21:41034806-41429078	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv544445	chr21:41034806-41429078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2837257	FSCN1	trans	parietal	SCAN
rs2837257	MORC3	cis	parietal	SCAN
rs2837257	B3GALT5	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41213600-41223600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:41220200-41223400	Weak transcription	Pancreas	Pancrea
3	chr21:41220200-41223600	Weak transcription	Gastric	stomach
4	chr21:41221200-41224000	Enhancers	Fetal Muscle Leg	muscle
5	chr21:41221800-41224800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr21:41222000-41225000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr21:41222000-41232400	Weak transcription	Right Ventricle	heart
8	chr21:41222200-41223800	Enhancers	Fetal Muscle Trunk	muscle
9	chr21:41222400-41223200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr21:41222400-41223800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr21:41222400-41223800	Enhancers	Fetal Brain Male	brain
12	chr21:41222600-41224000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr21:41222800-41223400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr21:41222800-41223600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr21:41222800-41223800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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