Variant report

Variant	rs13030108
Chromosome Location	chr2:20823612-20823613
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
2	chr2:20665733..20672605-chr2:20815236..20823686,12	MCF-7	breast:
3	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
4	chr2:20818029..20819883-chr2:20821089..20823704,2	K562	blood:

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1047176	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11676170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678019	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12470344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732149	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732152	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732154	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3732157	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]
rs3796065	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821217	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55788833	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56096206	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56174003	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56203116	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56240532	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336286	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6531247	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6719474	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6721558	0.94[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6723273	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6728166	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]
rs72782378	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72782380	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72782396	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784306	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7559305	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7586298	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7609280	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs896733	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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	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
10	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20815600-20824200	Enhancers	Fetal Heart	heart
4	chr2:20817000-20824200	Weak transcription	Thymus	Thymus
5	chr2:20817200-20826600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:20817400-20827200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:20817800-20826200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
14	chr2:20818000-20825600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:20818200-20823800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:20818200-20825200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:20818200-20828600	Weak transcription	Fetal Kidney	kidney
18	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:20818400-20825000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:20818400-20825600	Weak transcription	HUVEC	blood vessel
22	chr2:20818400-20828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:20818400-20828800	Weak transcription	Fetal Brain Male	brain
24	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:20818600-20824800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:20818600-20825600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:20818800-20824800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:20818800-20825200	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:20818800-20826200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:20818800-20833600	Weak transcription	A549	lung
31	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:20819200-20824600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:20819200-20825000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:20819200-20825400	Strong transcription	Primary B cells from cord blood	blood
36	chr2:20819200-20826200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:20819200-20827000	Strong transcription	Primary T cells from cord blood	blood
38	chr2:20819200-20827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:20819400-20824000	Weak transcription	Fetal Lung	lung
40	chr2:20819400-20824400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:20819400-20824800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr2:20819400-20825000	Strong transcription	NHLF	lung
43	chr2:20819400-20825600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:20819600-20824000	Weak transcription	Stomach Mucosa	stomach
47	chr2:20819600-20824600	Strong transcription	Brain Germinal Matrix	brain
48	chr2:20819600-20825000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr2:20819600-20825200	Strong transcription	Colonic Mucosa	Colon
50	chr2:20819600-20825200	Genic enhancers	Fetal Muscle Leg	muscle

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