Variant report

Variant	rs6728166
Chromosome Location	chr2:20814715-20814716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20812051..20815064-chr2:20816352..20817928,3	K562	blood:
2	chr2:20800330..20801246-chr2:20814133..20815002,3	MCF-7	breast:
3	chr2:20644675..20653597-chr2:20811663..20819940,20	MCF-7	breast:
4	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
5	chr2:20807683..20810867-chr2:20811760..20818347,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf43-4	chr2:20812057-20816027	NONHSAT069462

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1047176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676170	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678019	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11688002	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12470344	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13030108	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732149	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732152	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732154	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796065	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55788833	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56096206	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56174003	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56203116	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56240532	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56336286	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6531247	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6721558	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6723273	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782378	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782380	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782396	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72784306	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7559305	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7586298	0.95[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7609280	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs896733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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
2	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
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6728166	HS1BP3	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20805200-20816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:20808400-20816400	Enhancers	Rectal Smooth Muscle	rectum
3	chr2:20808400-20816600	Enhancers	Colon Smooth Muscle	Colon
4	chr2:20808400-20816800	Enhancers	Adipose Nuclei	Adipose
5	chr2:20808400-20819600	Enhancers	Fetal Muscle Leg	muscle
6	chr2:20808600-20818600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:20808600-20819400	Enhancers	Brain Anterior Caudate	brain
8	chr2:20808600-20819800	Enhancers	Brain Substantia Nigra	brain
9	chr2:20809000-20817200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr2:20809400-20816200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:20809600-20816600	Weak transcription	Fetal Thymus	thymus
12	chr2:20809600-20819200	Weak transcription	Primary T cells from cord blood	blood
13	chr2:20809800-20815000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:20810800-20819200	Weak transcription	Primary B cells from cord blood	blood
15	chr2:20810800-20819600	Enhancers	Brain Hippocampus Middle	brain
16	chr2:20811600-20816200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:20811600-20816200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:20811600-20820200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:20811800-20815800	Weak transcription	Fetal Kidney	kidney
20	chr2:20811800-20816000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:20811800-20816400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:20811800-20817200	Enhancers	HepG2	liver
23	chr2:20812000-20815600	Weak transcription	Fetal Heart	heart
24	chr2:20812200-20819200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:20812400-20816800	Enhancers	Spleen	Spleen
26	chr2:20812400-20817600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:20812400-20820600	Enhancers	Right Ventricle	heart
28	chr2:20812400-20820800	Enhancers	Right Atrium	heart
29	chr2:20812400-20821200	Enhancers	Left Ventricle	heart
30	chr2:20812600-20818200	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:20812600-20819200	Enhancers	Brain Angular Gyrus	brain
32	chr2:20812800-20819400	Enhancers	Fetal Lung	lung
33	chr2:20813000-20814800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:20813000-20815400	Enhancers	Gastric	stomach
35	chr2:20813000-20818200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:20813000-20818200	Enhancers	Fetal Intestine Large	intestine
37	chr2:20813000-20818400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:20813000-20818400	Enhancers	Lung	lung
39	chr2:20813000-20819000	Enhancers	Fetal Muscle Trunk	muscle
40	chr2:20813000-20819200	Enhancers	Esophagus	oesophagus
41	chr2:20813000-20819200	Enhancers	Psoas Muscle	Psoas
42	chr2:20813200-20814800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:20813200-20816800	Weak transcription	Fetal Brain Male	brain
44	chr2:20813400-20814800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:20813400-20814800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:20813400-20815000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:20813400-20815200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr2:20813400-20816400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr2:20813400-20817400	Enhancers	H1 Cell Line	embryonic stem cell
50	chr2:20813600-20814800	Enhancers	HMEC	breast

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