Variant report

Variant	rs11589914
Chromosome Location	chr1:153230954-153230955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153230941-153230991	PANC-1	pancreas:	n/a
2	chr1:153230907-153230957	SK-N-SH	brain:	n/a
3	chr1:153230941-153230991	HCT-116	colon:	n/a
4	chr1:153230941-153230991	H1-hESC	embryonic stem cell:	embryo
5	chr1:153230907-153230957	HEK293	kidney:	embryo
6	chr1:153230907-153230957	HPAEpiC	pulmonary alveolar:	n/a
7	chr1:153230907-153230957	AG09309	skin:	n/a
8	chr1:153230907-153230957	HL-60	blood:	n/a
9	chr1:153230941-153230991	BE2_C	brain:	n/a
10	chr1:153230941-153230991	ProgFib	skin:	n/a
11	chr1:153230907-153230957	AG10803	skin:	n/a
12	chr1:153230907-153230957	A549	lung:	n/a
13	chr1:153230941-153230991	MCF10A-Er-Src	breast:	n/a
14	chr1:153230941-153230991	Caco-2	colon:	n/a
15	chr1:153230907-153230957	ECC-1	luminal epithelium:	n/a
16	chr1:153230941-153230991	HAEpiC	amniotic membrane:	n/a
17	chr1:153230941-153230991	GM19239	blood:	n/a
18	chr1:153230941-153230991	HNPCEpiC	eye:	n/a
19	chr1:153230941-153230991	IMR90	lung:	fetal
20	chr1:153230941-153230991	HCF	heart:	n/a
21	chr1:153230907-153230957	GM12891	blood:	n/a
22	chr1:153230941-153230991	AG09319	gingival:	n/a
23	chr1:153230907-153230957	AG09319	gingival:	n/a
24	chr1:153230907-153230957	Hela-S3	cervix:	n/a
25	chr1:153230907-153230957	RPTEC	kidney:	n/a
26	chr1:153230907-153230957	HCF	heart:	n/a
27	chr1:153230941-153230991	BJ	skin:	n/a
28	chr1:153230941-153230991	NH-A	brain:	n/a
29	chr1:153230907-153230957	K562	blood:	n/a
30	chr1:153230941-153230991	T-47D	breast:	n/a
31	chr1:153230907-153230957	PANC-1	pancreas:	n/a
32	chr1:153230907-153230957	GM12878	blood:	n/a
33	chr1:153230907-153230957	NHBE	bronchial:	n/a
34	chr1:153230941-153230991	NHDF-neo	bronchial:	n/a
35	chr1:153230941-153230991	HL-60	blood:	n/a
36	chr1:153230907-153230957	AG04450	lung:	fetal
37	chr1:153230907-153230957	HEEpiC	esophagus:	n/a
38	chr1:153230941-153230991	AG09309	skin:	n/a
39	chr1:153230907-153230957	GM06990	blood:	n/a
40	chr1:153230907-153230957	HCPEpiC	choroid plexus:	n/a
41	chr1:153230907-153230957	NH-A	brain:	n/a
42	chr1:153230907-153230957	NHDF-neo	bronchial:	n/a
43	chr1:153230941-153230991	MCF-7	breast:	n/a
44	chr1:153230941-153230991	HRPEpiC	eye:	n/a
45	chr1:153230941-153230991	SKMC	muscle:	n/a
46	chr1:153230907-153230957	ProgFib	skin:	n/a
47	chr1:153230941-153230991	PrEC	prostate:	n/a
48	chr1:153230941-153230991	U87	brain:	n/a
49	chr1:153230941-153230991	SK-N-SH	brain:	n/a
50	chr1:153230941-153230991	SAEC	small airway:	n/a

No data

Variant related genes	Relation type
LOR	CpG island

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10159119	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10494292	0.83[CEU][hapmap]
rs10494293	0.83[CEU][hapmap]
rs10494294	0.83[CEU][hapmap]
rs10494295	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10494296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10494297	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10788862	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10888537	0.83[CEU][hapmap]
rs10888538	0.83[CEU][hapmap]
rs10888539	0.83[CEU][hapmap]
rs11205222	0.83[CEU][hapmap]
rs11205223	0.83[CEU][hapmap]
rs11205225	0.83[CEU][hapmap]
rs11205227	0.83[CEU][hapmap]
rs11205228	0.88[CEU][hapmap]
rs11205229	0.80[CEU][hapmap]
rs11205231	0.87[CEU][hapmap]
rs11205232	0.82[EUR][1000 genomes]
rs11205238	0.83[EUR][1000 genomes]
rs11205248	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11205251	0.83[LWK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs11205252	0.90[YRI][hapmap]
rs1143390	0.89[LWK][hapmap];0.93[YRI][hapmap]
rs11583156	0.82[EUR][1000 genomes]
rs11583609	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12043009	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069007	0.83[CEU][hapmap]
rs12122588	0.84[EUR][1000 genomes]
rs12127862	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs12134915	0.84[EUR][1000 genomes]
rs12136409	0.83[EUR][1000 genomes]
rs12142970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12747804	0.83[EUR][1000 genomes]
rs12760683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1329099	0.83[EUR][1000 genomes]
rs1329100	0.83[EUR][1000 genomes]
rs1410859	0.83[CEU][hapmap]
rs16835073	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs16835081	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs16835083	0.83[EUR][1000 genomes]
rs16835093	0.83[CEU][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes]
rs2094638	0.89[YRI][hapmap]
rs34119886	0.83[EUR][1000 genomes]
rs35358388	0.83[EUR][1000 genomes]
rs71626758	0.83[EUR][1000 genomes]
rs7538295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs873234	0.90[YRI][hapmap]

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	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003014	chr1:153209833-153263691	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv535172	chr1:153209833-153263691	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv998032	chr1:153210770-153264131	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11589914	HIST2H2AC	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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