Variant report

Variant	rs12058979
Chromosome Location	chr1:10004350-10004351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10002537-10004391	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9884569..9887155-chr1:10002902..10004455,2	K562	blood:
2	chr1:10002125..10006916-chr1:10090169..10095056,10	K562	blood:
3	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
4	chr1:9969188..9972816-chr1:10001560..10005397,4	MCF-7	breast:
5	chr1:10002086..10005062-chr1:10091281..10093134,5	K562	blood:
6	chr1:10002061..10004916-chr1:10091716..10094596,6	MCF-7	breast:
7	chr1:9969022..9974825-chr1:10002123..10006220,12	K562	blood:
8	chr1:9968043..9973723-chr1:10001891..10008599,10	K562	blood:
9	chr1:10002273..10004549-chr1:10490535..10492203,2	MCF-7	breast:
10	chr1:9992820..9997928-chr1:9999758..10004449,8	K562	blood:
11	chr1:10001294..10005828-chr1:10093316..10096471,4	K562	blood:
12	chr1:10003032..10004962-chr1:10118663..10120416,2	MCF-7	breast:
13	chr1:9881807..9884566-chr1:10002290..10004897,3	K562	blood:
14	chr1:9969199..9972073-chr1:10003014..10005092,3	MCF-7	breast:
15	chr1:9881807..9884566-chr1:10002965..10004897,2	K562	blood:

No data

Variant related genes	Relation type
LZIC	TF binding region
RN7SKP269	TF binding region
ENSG00000251503	Chromatin interaction
ENSG00000233623	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000130939	Chromatin interaction
ENSG00000171603	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000271989	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11121501	0.98[AMR][1000 genomes]
rs11121509	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12059092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060375	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12062953	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]
rs12064822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12065908	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12070725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12071307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12082318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12086598	0.98[AMR][1000 genomes]
rs12088598	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12094254	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12097182	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17034440	0.80[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2289478	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2297843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4845912	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4846104	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4846108	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4846187	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs60132751	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61743470	0.98[AMR][1000 genomes]
rs6663059	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6664208	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7516611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7535945	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv947175	chr1:9996275-10009860	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12058979	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10002200-10004400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:10002200-10004400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:10002200-10004400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:10002200-10004400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:10002200-10004400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:10002200-10004400	Active TSS	Fetal Intestine Small	intestine
7	chr1:10002200-10004400	Active TSS	Rectal Smooth Muscle	rectum
8	chr1:10002200-10004400	Active TSS	GM12878-XiMat	blood
9	chr1:10002200-10004400	Active TSS	K562	blood
10	chr1:10002400-10004400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:10002400-10004400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:10002400-10004400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:10002400-10004400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:10002400-10004400	Active TSS	Brain Angular Gyrus	brain
15	chr1:10002400-10004400	Active TSS	Fetal Intestine Large	intestine
16	chr1:10002400-10004400	Active TSS	Placenta Amnion	Placenta Amnion
17	chr1:10002400-10004400	Active TSS	Hela-S3	cervix
18	chr1:10002400-10004400	Active TSS	NHLF	lung
19	chr1:10002400-10004600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:10002400-10004600	Active TSS	Right Ventricle	heart
21	chr1:10002400-10004600	Active TSS	A549	lung
22	chr1:10002400-10004600	Active TSS	HSMMtube	muscle
23	chr1:10002400-10004800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:10002400-10004800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:10002600-10004400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:10002600-10004400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:10002600-10004400	Active TSS	Brain Anterior Caudate	brain
28	chr1:10002600-10004400	Active TSS	Colonic Mucosa	Colon
29	chr1:10002600-10004400	Active TSS	Esophagus	oesophagus
30	chr1:10002600-10004400	Active TSS	HMEC	breast
31	chr1:10002600-10004600	Active TSS	Osteobl	bone
32	chr1:10002800-10004400	Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr1:10002800-10004400	Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:10002800-10004400	Active TSS	Brain Cingulate Gyrus	brain
35	chr1:10002800-10004400	Active TSS	Brain Substantia Nigra	brain
36	chr1:10002800-10004400	Active TSS	Duodenum Mucosa	Duodenum
37	chr1:10002800-10004400	Active TSS	HSMM	muscle
38	chr1:10002800-10004400	Active TSS	NHEK	skin
39	chr1:10003000-10004400	Active TSS	Primary T cells from cord blood	blood
40	chr1:10003000-10004400	Active TSS	Liver	Liver
41	chr1:10003000-10004400	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr1:10003000-10004400	Active TSS	HUVEC	blood vessel
43	chr1:10003200-10004400	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:10003600-10004400	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr1:10003600-10004400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:10003800-10004400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr1:10003800-10004400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr1:10003800-10004400	Flanking Active TSS	Placenta	Placenta
49	chr1:10003800-10004400	Active TSS	Right Atrium	heart
50	chr1:10003800-10004600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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