Variant report

Variant	rs341053
Chromosome Location	chr11:72390640-72390641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72388590..72390821-chr11:72491709..72494261,2	MCF-7	breast:
2	chr11:72388034..72392133-chr11:72393186..72397535,6	MCF-7	breast:
3	chr11:72389749..72392424-chr11:72399427..72400937,2	K562	blood:
4	chr11:72390061..72391638-chr11:72391998..72394239,2	MCF-7	breast:
5	chr11:72385920..72387778-chr11:72388212..72390871,2	K562	blood:
6	chr11:72383575..72386768-chr11:72389731..72393141,4	K562	blood:
7	chr11:72351275..72353483-chr11:72388589..72391292,2	K562	blood:

Variant related genes	Relation type
ENSG00000214530	Chromatin interaction
ENSG00000186642	Chromatin interaction
ENSG00000186635	Chromatin interaction
ENSG00000256007	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10793036	0.81[CHB][hapmap]
rs10898866	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs11235557	0.85[ASN][1000 genomes]
rs11235558	0.85[ASN][1000 genomes]
rs11235559	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs11235569	0.85[CEU][hapmap]
rs11235575	0.92[CEU][hapmap]
rs11607038	0.84[JPT][hapmap]
rs12146545	1.00[CHB][hapmap]
rs12362256	0.83[ASN][1000 genomes]
rs12363065	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs12576046	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12576058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12786302	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12787293	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12797368	0.85[ASN][1000 genomes]
rs12797791	0.93[CHB][hapmap]
rs12799451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12802369	0.96[ASN][1000 genomes]
rs12804316	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1391888	1.00[CHB][hapmap]
rs163694	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs168175	0.82[ASN][1000 genomes]
rs1872126	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs189332	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1980089	0.81[CHB][hapmap]
rs2035467	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2037030	0.85[ASN][1000 genomes]
rs2291289	0.85[CEU][hapmap]
rs2306607	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs2306609	0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2306616	0.84[JPT][hapmap]
rs341052	0.93[CHB][hapmap]
rs341060	0.87[ASN][1000 genomes]
rs341061	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs341062	0.86[ASN][1000 genomes]
rs34142547	0.97[ASN][1000 genomes]
rs342322	0.85[ASN][1000 genomes]
rs34285624	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34802028	0.97[ASN][1000 genomes]
rs35748558	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3758934	0.91[ASN][1000 genomes]
rs3758935	0.92[ASN][1000 genomes]
rs3758936	0.92[ASN][1000 genomes]
rs3781913	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs3781916	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs458275	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs458575	0.81[CHB][hapmap]
rs7125221	0.88[CEU][hapmap]
rs7126790	0.91[ASN][1000 genomes]
rs900613	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs900614	0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs900615	0.88[ASN][1000 genomes]
rs90409	0.86[CHB][hapmap]

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	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
3	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs341053	STARD10	cis	multi-tissue	Pritchard
rs341053	ARAP1	cis	cerebellum	SCAN
rs341053	NADSYN1	cis	cerebellum	SCAN
rs341053	KRTAP5-10	cis	parietal	SCAN
rs341053	UVRAG	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72380600-72395400	Weak transcription	Right Atrium	heart
2	chr11:72385400-72394600	Weak transcription	Gastric	stomach
3	chr11:72388000-72394400	Weak transcription	Brain Substantia Nigra	brain
4	chr11:72388000-72397200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:72388200-72391600	Weak transcription	Brain Angular Gyrus	brain
6	chr11:72388200-72396400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:72388400-72390800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:72388400-72391400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:72388400-72391800	Weak transcription	Ovary	ovary
10	chr11:72388600-72391200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:72388600-72392400	Weak transcription	Pancreas	Pancrea
12	chr11:72388600-72395000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:72388600-72396000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:72388800-72392000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:72389600-72397800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:72389800-72394000	Weak transcription	Thymus	Thymus
17	chr11:72390000-72392800	Enhancers	Right Ventricle	heart
18	chr11:72390000-72394400	Weak transcription	GM12878-XiMat	blood
19	chr11:72390000-72394600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:72390000-72395200	Weak transcription	Liver	Liver
21	chr11:72390000-72397000	Weak transcription	Primary B cells from cord blood	blood
22	chr11:72390200-72394200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:72390200-72394600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:72390200-72397800	Weak transcription	HepG2	liver
25	chr11:72390400-72391200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr11:72390400-72392800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:72390400-72395200	Weak transcription	A549	lung
28	chr11:72390600-72390800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
29	chr11:72390600-72390800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:72390600-72391400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:72390600-72391800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:72390600-72395400	Weak transcription	Rectal Mucosa Donor 29	rectum

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