Variant report

Variant	rs12062953
Chromosome Location	chr1:10009925-10009926
allele	C/T
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10008573..10013502-chr1:10090291..10096219,9	MCF-7	breast:
2	chr1:10009350..10011460-chr1:10068351..10069869,2	K562	blood:
3	chr1:10006856..10008883-chr1:10008961..10010620,2	K562	blood:
4	chr1:10009323..10011578-chr1:10096303..10099000,2	MCF-7	breast:
5	chr1:10008967..10010504-chr1:10091583..10094511,2	MCF-7	breast:
6	chr1:9988737..9991346-chr1:10009208..10011504,2	K562	blood:
7	chr1:10009468..10012009-chr1:10018654..10021337,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMNAT1-1	chr1:10009696-10010032	ENSG00000228150.1

No data

Variant related genes	Relation type
ENSG00000202415	Chromatin interaction
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11121501	0.95[AMR][1000 genomes]
rs11121509	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11801898	0.80[ASN][1000 genomes]
rs12058979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12059092	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12060375	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12064822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065908	1.00[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12070725	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12082318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12086598	0.95[AMR][1000 genomes]
rs12088598	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12094254	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12097182	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17034440	0.84[MEX][hapmap];0.87[TSI][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2289478	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2297843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4845912	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4846104	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4846108	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4846187	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs60132751	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61743470	0.95[AMR][1000 genomes]
rs6663059	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6664208	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7516611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7535945	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12062953	LZIC	cis	lymphoblastoid	seeQTL
rs12062953	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10004000-10010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:10004000-10010600	Weak transcription	Fetal Heart	heart
3	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
4	chr1:10004200-10010000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:10004200-10010400	Weak transcription	Fetal Lung	lung
6	chr1:10004200-10010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:10004200-10010600	Weak transcription	Fetal Brain Male	brain
8	chr1:10004200-10010600	Weak transcription	Fetal Kidney	kidney
9	chr1:10004200-10010600	Weak transcription	Ovary	ovary
10	chr1:10004200-10011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:10004200-10019400	Weak transcription	NH-A	brain
12	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:10004200-10033800	Weak transcription	Gastric	stomach
14	chr1:10004400-10010000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:10004400-10010000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:10004400-10010000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:10004400-10010000	Weak transcription	Stomach Mucosa	stomach
18	chr1:10004400-10010200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:10004400-10010200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:10004400-10010200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:10004400-10010200	Weak transcription	Placenta	Placenta
22	chr1:10004400-10010400	Weak transcription	Esophagus	oesophagus
23	chr1:10004400-10010600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:10004400-10010600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:10004400-10010600	Weak transcription	Fetal Brain Female	brain
26	chr1:10004400-10010600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:10004400-10010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:10004400-10018200	Weak transcription	NHLF	lung
29	chr1:10004400-10021200	Weak transcription	HSMM	muscle
30	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
31	chr1:10004600-10010400	Weak transcription	Primary T cells from cord blood	blood
32	chr1:10004600-10010400	Weak transcription	Thymus	Thymus
33	chr1:10004600-10010600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:10004600-10010600	Weak transcription	NHDF-Ad	bronchial
35	chr1:10004600-10010600	Weak transcription	Osteobl	bone
36	chr1:10004600-10021000	Weak transcription	HSMMtube	muscle
37	chr1:10004600-10032400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:10004800-10010000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:10004800-10010000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:10004800-10010000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:10004800-10010000	Weak transcription	Brain Anterior Caudate	brain
42	chr1:10004800-10010200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:10004800-10010200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:10004800-10010200	Weak transcription	Left Ventricle	heart
45	chr1:10004800-10010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:10004800-10010600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:10004800-10010600	Weak transcription	Right Ventricle	heart
48	chr1:10004800-10010600	Weak transcription	Dnd41	blood
49	chr1:10004800-10010600	Weak transcription	Hela-S3	cervix
50	chr1:10004800-10010600	Weak transcription	NHEK	skin

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