Variant report

Variant	rs10191983
Chromosome Location	chr2:20679101-20679102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20676371..20679223-chr2:20692816..20695545,2	K562	blood:
2	chr2:20677229..20679285-chr2:20689494..20691945,2	K562	blood:
3	chr2:20678236..20680234-chr2:20683547..20685261,2	MCF-7	breast:
4	chr2:20643286..20659825-chr2:20662702..20680153,143	MCF-7	breast:
5	chr2:20670475..20680240-chr2:20690452..20700902,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10856799	0.81[EUR][1000 genomes]
rs11675571	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11898154	0.81[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11901246	0.87[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs12467898	0.89[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12478968	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12997261	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13021908	0.81[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1872070	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2084919	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2348707	0.83[EUR][1000 genomes]
rs342124	0.85[GIH][hapmap]
rs4666401	0.81[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4666407	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666408	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4666409	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704834	0.81[AMR][1000 genomes]
rs7601359	0.84[EUR][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	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873723	chr2:20678000-20720237	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv873724	chr2:20678000-20757286	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10191983	FAM49A	cis	cerebellum	SCAN
rs10191983	HS1BP3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20666400-20681800	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:20672000-20681800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:20673000-20687000	Weak transcription	Spleen	Spleen
4	chr2:20673400-20682000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:20673400-20683400	Weak transcription	Esophagus	oesophagus
6	chr2:20674400-20682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:20674600-20680800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:20674600-20681800	Weak transcription	Fetal Kidney	kidney
9	chr2:20674600-20686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:20674800-20682000	Weak transcription	Adipose Nuclei	Adipose
11	chr2:20674800-20682000	Weak transcription	Left Ventricle	heart
12	chr2:20675400-20681600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:20676000-20679800	Weak transcription	Liver	Liver
14	chr2:20678200-20681600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:20678600-20679200	Enhancers	Brain Cingulate Gyrus	brain
16	chr2:20678600-20679400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr2:20678600-20679600	Enhancers	Fetal Muscle Leg	muscle
18	chr2:20678600-20680200	Enhancers	Brain Substantia Nigra	brain
19	chr2:20678800-20679200	Enhancers	Brain Angular Gyrus	brain
20	chr2:20678800-20679400	Enhancers	Brain Anterior Caudate	brain
21	chr2:20678800-20679800	Enhancers	Brain Hippocampus Middle	brain
22	chr2:20678800-20679800	Enhancers	Psoas Muscle	Psoas
23	chr2:20679000-20680000	Enhancers	Skeletal Muscle Male	skeletal muscle

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