Variant report

Variant	rs12997261
Chromosome Location	chr2:20682303-20682304
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20674640..20676762-chr2:20681845..20683748,2	MCF-7	breast:
2	chr2:20648526..20656143-chr2:20680792..20689222,12	MCF-7	breast:
3	chr2:20645409..20653526-chr2:20681713..20692568,21	MCF-7	breast:
4	chr2:20645621..20648326-chr2:20680840..20682553,2	K562	blood:
5	chr2:20673986..20676261-chr2:20681219..20683452,2	K562	blood:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10191983	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]
rs10856799	0.82[AMR][1000 genomes]
rs11675571	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11898154	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs11901246	0.82[AMR][1000 genomes]
rs12467898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478968	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13016649	1.00[ASW][hapmap];0.84[CHD][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13021908	0.82[AMR][1000 genomes]
rs2084919	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4666401	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs4666407	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4666408	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4666409	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7601359	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12997261	HS1BP3	cis	parietal	SCAN
rs12997261	FAM49A	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20673000-20687000	Weak transcription	Spleen	Spleen
2	chr2:20673400-20683400	Weak transcription	Esophagus	oesophagus
3	chr2:20674600-20686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:20679200-20683000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:20679200-20684000	Weak transcription	Brain Angular Gyrus	brain
6	chr2:20679400-20683400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:20679800-20683600	Weak transcription	Psoas Muscle	Psoas
8	chr2:20680000-20682800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:20680800-20686200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:20681600-20682400	Enhancers	Rectal Smooth Muscle	rectum
11	chr2:20681600-20683600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:20681600-20684200	Enhancers	Ovary	ovary
13	chr2:20681600-20684200	Enhancers	Right Atrium	heart
14	chr2:20681800-20682400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:20681800-20682400	Enhancers	Brain Anterior Caudate	brain
16	chr2:20681800-20683200	Enhancers	Fetal Kidney	kidney
17	chr2:20681800-20684200	Enhancers	Colon Smooth Muscle	Colon
18	chr2:20681800-20684400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:20682000-20682600	Enhancers	Fetal Muscle Leg	muscle
20	chr2:20682000-20683400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:20682000-20683600	Enhancers	Left Ventricle	heart
22	chr2:20682000-20684200	Enhancers	Adipose Nuclei	Adipose
23	chr2:20682000-20684200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:20682000-20685800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:20682200-20682400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:20682200-20682400	Enhancers	Brain Hippocampus Middle	brain
27	chr2:20682200-20682400	Enhancers	Brain Substantia Nigra	brain
28	chr2:20682200-20684000	Enhancers	Aorta	Aorta
29	chr2:20682200-20684400	Weak transcription	Right Ventricle	heart

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