Variant report

Variant	rs2712788
Chromosome Location	chr11:74816492-74816493
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74812003..74816154-chr11:74816263..74818470,5	K562	blood:
2	chr11:74813734..74816663-chr11:74951389..74954189,2	K562	blood:
3	chr11:74805066..74808860-chr11:74814569..74816963,4	K562	blood:
4	chr11:74790767..74792368-chr11:74814886..74816678,2	K562	blood:
5	chr11:74815946..74818124-chr11:74820163..74822127,2	K562	blood:

Variant related genes	Relation type
ENSG00000261594	Chromatin interaction
ENSG00000213333	Chromatin interaction
ENSG00000255136	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10899075	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1944614	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1944615	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1944616	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs2712786	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712794	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2712797	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2712800	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap]
rs2712801	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2712809	0.85[JPT][hapmap]
rs2712811	0.85[JPT][hapmap]
rs2712818	0.81[CEU][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs2851069	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2851071	0.85[JPT][hapmap]
rs2851072	0.85[JPT][hapmap]
rs2851076	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851077	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851079	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851081	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851082	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851086	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851103	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2851104	0.82[CHB][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap]
rs2851107	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4435030	0.94[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs870505	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs870506	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs875482	0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs949071	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3478707	chr11:74782633-74842791	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	esv3478718	chr11:74782633-74842791	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2712788	UVRAG	cis	lymphoblastoid	seeQTL
rs2712788	XRRA1	cis	cerebellum	SCAN
rs2712788	RNF169	cis	cerebellum	SCAN
rs2712788	INPPL1	cis	parietal	SCAN
rs2712788	THRSP	cis	parietal	SCAN
rs2712788	XRRA1	cis	lymphoblastoid	seeQTL
rs2712788	FCHSD2	cis	cerebellum	SCAN
rs2712788	FMN2	trans	cerebellum	SCAN
rs2712788	XRRA1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74811600-74818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:74811800-74816600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr11:74811800-74816600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:74814800-74818200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:74815000-74818000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:74815200-74816600	Weak transcription	Osteobl	bone
7	chr11:74815200-74817600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:74815200-74818200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:74815200-74818200	Weak transcription	NHDF-Ad	bronchial
10	chr11:74815200-74818200	Weak transcription	NHLF	lung
11	chr11:74815400-74816600	Weak transcription	GM12878-XiMat	blood
12	chr11:74816000-74816600	Enhancers	A549	lung
13	chr11:74816200-74817000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:74816200-74817000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:74816200-74817000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr11:74816200-74817000	Flanking Active TSS	K562	blood
17	chr11:74816400-74816800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:74816400-74816800	Enhancers	NH-A	brain
19	chr11:74816400-74817000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr11:74816400-74817000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:74816400-74817000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr11:74816400-74819000	Enhancers	Muscle Satellite Cultured Cells	--

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