Variant report

Variant	rs11888857
Chromosome Location	chr2:51673576-51673577
allele	A/C
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	2:51664217-51674289..2:52112664-52117037	K562	blood:
2	2:51664217-51674289..2:52043909-52049825	H1-hESC	embryonic stem cell:	embryo
3	2:51664217-51674289..2:52034460-52043624	GM12878	blood:
4	2:51664217-51674289..2:52100874-52104046	H1-hESC	embryonic stem cell:	embryo
5	2:51664217-51674289..2:52006946-52008886	H1-hESC	embryonic stem cell:	embryo
6	2:51664217-51674289..2:51745267-51754233	H1-hESC	embryonic stem cell:	embryo
7	2:51664217-51674289..2:51983874-51990011	GM12878	blood:
8	2:51664217-51674289..2:52055539-52058793	H1-hESC	embryonic stem cell:	embryo
9	2:51664217-51674289..2:51764739-51769547	H1-hESC	embryonic stem cell:	embryo
10	2:51664217-51674289..2:51908308-51914662	H1-hESC	embryonic stem cell:	embryo
11	2:51664217-51674289..2:51733860-51734854	H1-hESC	embryonic stem cell:	embryo
12	2:51664217-51674289..2:52132828-52140118	H1-hESC	embryonic stem cell:	embryo
13	2:51664217-51674289..2:51674430-51675236	H1-hESC	embryonic stem cell:	embryo
14	2:51664217-51674289..2:51887872-51889464	H1-hESC	embryonic stem cell:	embryo
15	2:51664217-51674289..2:51974300-51979334	H1-hESC	embryonic stem cell:	embryo
16	2:51664217-51674289..2:51942985-51943865	H1-hESC	embryonic stem cell:	embryo

No data

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10207943	0.92[EUR][1000 genomes]
rs10221616	0.81[EUR][1000 genomes]
rs11563050	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12995306	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13001371	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13001835	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006383	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011380	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011925	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012168	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13012231	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13020816	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030070	0.92[EUR][1000 genomes]
rs13036132	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528804	0.84[GIH][hapmap]
rs1919427	0.85[GIH][hapmap]
rs28957374	0.89[ASN][1000 genomes]
rs28958871	0.85[ASN][1000 genomes]
rs28958872	0.89[ASN][1000 genomes]
rs6721908	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734029	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737158	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737381	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591147	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007188	chr2:51135645-51821787	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535704	chr2:51135645-51821787	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1005168	chr2:51142848-51702008	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv535705	chr2:51142848-51702008	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv948449	chr2:51152019-51735494	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1001552	chr2:51225970-52139741	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv535708	chr2:51225970-52139741	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1011583	chr2:51382812-51702008	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv535711	chr2:51382812-51702008	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv821624	chr2:51513925-51844864	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv874066	chr2:51554047-51680489	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv581879	chr2:51639748-51673576	Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv3446801	chr2:51659396-51678205	Active TSS ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv527513	chr2:51673576-51693598	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11888857	MTIF2	cis	cerebellum	SCAN
rs11888857	MTIF2	cis	parietal	SCAN
rs11888857	NRXN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:51672400-51677800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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