Variant report

Variant	rs10878598
Chromosome Location	chr12:67712768-67712769
allele	A/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:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:67707980..67709583-chr12:67712739..67715234,2	K562	blood:
2	chr12:67712594..67714797-chr12:132194188..132196961,2	MCF-7	breast:
3	chr12:67662013..67664268-chr12:67712332..67714584,2	K562	blood:
4	chr12:67664539..67666217-chr12:67712484..67714487,2	K562	blood:
5	chr12:67708442..67711026-chr12:67711731..67713764,2	MCF-7	breast:
6	chr12:67712478..67714489-chr12:67715652..67718009,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DYRK2-3	chr12:67711527-67713730	ENSG00000247008
2	lnc-DYRK2-3	chr12:67711527-67713732	NONHSAT029248

No data

Variant related genes	Relation type
ENSG00000061936	Chromatin interaction
ENSG00000111530	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11176668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11176670	0.95[ASN][1000 genomes]
rs11176673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176689	1.00[ASN][1000 genomes]
rs11176703	1.00[ASN][1000 genomes]
rs11176704	1.00[ASN][1000 genomes]
rs11176705	1.00[ASN][1000 genomes]
rs11176707	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176711	0.95[ASN][1000 genomes]
rs12302564	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305377	1.00[ASN][1000 genomes]
rs12306657	1.00[ASN][1000 genomes]
rs12311150	0.95[ASN][1000 genomes]
rs12314146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3736630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55646172	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55809526	0.95[ASN][1000 genomes]
rs55809587	0.95[ASN][1000 genomes]
rs55906716	0.95[ASN][1000 genomes]
rs55978724	0.95[ASN][1000 genomes]
rs56224819	0.95[ASN][1000 genomes]
rs56728872	0.95[ASN][1000 genomes]
rs58114937	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60009568	1.00[ASN][1000 genomes]
rs60072946	0.95[ASN][1000 genomes]
rs60077199	1.00[ASN][1000 genomes]
rs60104343	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60971316	1.00[ASN][1000 genomes]
rs61195985	0.95[ASN][1000 genomes]
rs61219299	1.00[ASN][1000 genomes]
rs61281993	1.00[ASN][1000 genomes]
rs7137520	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7296364	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7298244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7307353	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312708	0.95[ASN][1000 genomes]
rs7954050	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7976686	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv756	chr12:67703587-67744743	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67681000-67714200	Weak transcription	Spleen	Spleen
2	chr12:67682200-67715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:67686000-67717000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:67686200-67716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:67686400-67716000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:67687800-67715400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:67688200-67717000	Strong transcription	NH-A	brain
8	chr12:67688400-67716000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:67691000-67716000	Weak transcription	Fetal Intestine Small	intestine
10	chr12:67698600-67714000	Strong transcription	Fetal Thymus	thymus
11	chr12:67700000-67713200	Weak transcription	Pancreas	Pancrea
12	chr12:67700000-67715400	Weak transcription	Lung	lung
13	chr12:67700000-67716200	Weak transcription	Fetal Stomach	stomach
14	chr12:67700200-67717600	Weak transcription	Gastric	stomach
15	chr12:67700400-67712800	Weak transcription	Ovary	ovary
16	chr12:67700600-67716000	Weak transcription	Aorta	Aorta
17	chr12:67700600-67717400	Weak transcription	Psoas Muscle	Psoas
18	chr12:67702800-67714600	Weak transcription	Small Intestine	intestine
19	chr12:67706200-67716400	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:67706600-67714200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:67706600-67716200	Weak transcription	Fetal Heart	heart
22	chr12:67706600-67720600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:67706800-67712800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:67706800-67713200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:67706800-67713400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:67706800-67714400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:67706800-67714600	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:67706800-67714800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:67706800-67716600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:67707400-67714400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:67707800-67714200	Weak transcription	Brain Germinal Matrix	brain
32	chr12:67708000-67714600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:67708200-67714400	Weak transcription	K562	blood
34	chr12:67708200-67714600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:67708200-67715000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:67708400-67713200	Weak transcription	Fetal Lung	lung
37	chr12:67708600-67714200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:67708600-67714200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:67708600-67716400	Weak transcription	NHDF-Ad	bronchial
40	chr12:67708800-67714000	Weak transcription	Primary B cells from cord blood	blood
41	chr12:67708800-67714200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:67708800-67714400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:67708800-67714800	Weak transcription	Adipose Nuclei	Adipose
44	chr12:67708800-67715000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:67708800-67717200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:67708800-67717800	Weak transcription	Brain Anterior Caudate	brain
47	chr12:67709000-67714800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:67709000-67715800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:67709400-67712800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:67709800-67713400	Strong transcription	Dnd41	blood

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