Variant report

Variant	rs11205347
Chromosome Location	chr1:150210120-150210121
allele	C/T
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:12)
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	chr1:150209922-150210453	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150039411..150040952-chr1:150209636..150212635,2	K562	blood:
2	chr1:150203436..150211066-chr1:150333611..150339492,20	K562	blood:
3	chr1:150207085..150210384-chr1:150292615..150294360,3	K562	blood:
4	chr1:150206250..150210524-chr1:150335148..150338813,9	MCF-7	breast:
5	chr1:150205879..150210456-chr1:150251557..150256195,8	MCF-7	breast:
6	chr1:149857476..149860799-chr1:150206355..150210783,8	K562	blood:
7	chr1:150207682..150210552-chr1:150291812..150294121,3	K562	blood:
8	chr1:150198495..150205043-chr1:150206226..150211170,11	MCF-7	breast:
9	chr1:150209725..150211414-chr1:150230060..150232543,2	K562	blood:
10	chr1:150209914..150212517-chr1:150228634..150232834,3	K562	blood:
11	chr1:150205053..150211036-chr1:150333116..150338498,15	K562	blood:
12	chr1:150206579..150210456-chr1:150238390..150242863,9	MCF-7	breast:

No data

Variant related genes	Relation type
ANP32E	TF binding region
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000159208	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000118292	Chromatin interaction
ENSG00000117362	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000117360	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10788872	0.92[ASN][1000 genomes]
rs10888574	0.81[EUR][1000 genomes]
rs10888575	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888576	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11205339	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11205340	0.91[ASN][1000 genomes]
rs11205341	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs11205343	0.92[ASN][1000 genomes]
rs11205348	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11205350	0.81[EUR][1000 genomes]
rs11811787	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12131063	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12133235	0.85[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12133238	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12569047	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13374013	0.81[EUR][1000 genomes]
rs13374483	0.81[EUR][1000 genomes]
rs1535873	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1924549	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2038752	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2038753	0.96[ASN][1000 genomes]
rs3118124	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3121000	0.88[ASN][1000 genomes]
rs3121001	0.91[ASN][1000 genomes]
rs3754048	0.82[CEU][hapmap]
rs3850839	0.83[CEU][hapmap]
rs4408187	0.91[ASN][1000 genomes]
rs55647200	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55956539	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59507173	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61161619	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587753	0.96[ASN][1000 genomes]
rs6655935	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6660127	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6665499	0.86[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6668679	0.81[EUR][1000 genomes]
rs6680040	0.86[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6682434	0.92[ASN][1000 genomes]
rs6692738	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694215	0.96[ASN][1000 genomes]
rs6703332	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7522034	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs7532164	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535712	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7548543	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs7550600	0.86[EUR][1000 genomes]
rs7551023	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555995	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	164 gene(s)	inside rSNPs	diseases
3	esv3452492	chr1:150210095-150211365	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3452493	chr1:150210095-150211365	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11205347	TNFAIP8L2	cis	cerebellum	SCAN
rs11205347	MRPS21	cis	cerebellum	SCAN
rs11205347	MRPS21	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150209000-150212000	Weak transcription	Lung	lung
2	chr1:150209200-150215400	Weak transcription	Right Atrium	heart
3	chr1:150209400-150210400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:150209400-150212000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:150209600-150210200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:150209600-150210400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:150209600-150212000	Weak transcription	HepG2	liver
8	chr1:150209600-150212200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:150209600-150212400	Weak transcription	GM12878-XiMat	blood
10	chr1:150209800-150210200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:150209800-150210200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:150210000-150214800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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