Variant report

Variant	rs6719474
Chromosome Location	chr2:20812204-20812205
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20811207..20813551-chr2:20816352..20818633,2	K562	blood:
2	chr2:20791915..20794590-chr2:20811997..20814487,2	MCF-7	breast:
3	chr2:20807940..20810895-chr2:20811294..20813861,2	K562	blood:
4	chr2:20770603..20772364-chr2:20811267..20812996,2	K562	blood:
5	chr2:20812051..20815064-chr2:20816352..20817928,3	K562	blood:
6	chr2:20810389..20812991-chr2:20823775..20826259,2	MCF-7	breast:
7	chr2:20644675..20653597-chr2:20811663..20819940,20	MCF-7	breast:
8	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
9	chr2:20807683..20810867-chr2:20811760..20818347,7	MCF-7	breast:

(count:1 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000118960	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 37 )
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[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676170	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11678019	0.89[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11688002	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12470344	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13030108	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732149	0.94[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732152	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732154	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796065	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3821217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55788833	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56096206	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56174003	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56203116	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56240532	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56336286	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6531247	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721558	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6723273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6728166	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]
rs72782378	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72782380	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72782396	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72784306	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7559305	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586298	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7609280	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs896733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6719474	HS1BP3	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20803200-20814000	Weak transcription	HSMM	muscle
2	chr2:20804400-20813400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:20805200-20813600	Weak transcription	HMEC	breast
4	chr2:20805200-20813800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:20805200-20814000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:20805200-20816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:20808400-20813600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:20808400-20814200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:20808400-20816400	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:20808400-20816600	Enhancers	Colon Smooth Muscle	Colon
11	chr2:20808400-20816800	Enhancers	Adipose Nuclei	Adipose
12	chr2:20808400-20819600	Enhancers	Fetal Muscle Leg	muscle
13	chr2:20808600-20812400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:20808600-20818600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:20808600-20819400	Enhancers	Brain Anterior Caudate	brain
16	chr2:20808600-20819800	Enhancers	Brain Substantia Nigra	brain
17	chr2:20809000-20817200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:20809200-20813000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:20809400-20816200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr2:20809600-20812600	Weak transcription	Fetal Brain Female	brain
21	chr2:20809600-20813000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:20809600-20813400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:20809600-20813600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:20809600-20813800	Weak transcription	NHEK	skin
25	chr2:20809600-20814000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:20809600-20814200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:20809600-20814200	Weak transcription	Brain Germinal Matrix	brain
28	chr2:20809600-20816600	Weak transcription	Fetal Thymus	thymus
29	chr2:20809600-20819200	Weak transcription	Primary T cells from cord blood	blood
30	chr2:20809800-20813400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:20809800-20814000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:20809800-20815000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:20810000-20812600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:20810000-20812600	Weak transcription	Fetal Brain Male	brain
35	chr2:20810000-20813000	Weak transcription	Esophagus	oesophagus
36	chr2:20810000-20814400	Weak transcription	Small Intestine	intestine
37	chr2:20810400-20814400	Enhancers	HUVEC	blood vessel
38	chr2:20810600-20812600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:20810600-20814000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:20810800-20819200	Weak transcription	Primary B cells from cord blood	blood
41	chr2:20810800-20819600	Enhancers	Brain Hippocampus Middle	brain
42	chr2:20811600-20812600	Weak transcription	Brain Angular Gyrus	brain
43	chr2:20811600-20813400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:20811600-20813400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:20811600-20813600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:20811600-20813600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:20811600-20813800	Weak transcription	K562	blood
48	chr2:20811600-20814200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:20811600-20814400	Weak transcription	Aorta	Aorta
50	chr2:20811600-20816200	Weak transcription	Primary hematopoietic stem cells	blood

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