Variant report

Variant	rs1135029
Chromosome Location	chr11:72289291-72289292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72287726..72290086-chr11:72293581..72295527,2	K562	blood:
2	chr11:72283857..72286700-chr11:72287444..72290426,4	MCF-7	breast:
3	chr11:72288586..72291436-chr11:72293581..72295884,2	K562	blood:

Variant related genes	Relation type
ENSG00000256633	Chromatin interaction
ENSG00000186642	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10793036	0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.87[ASN][1000 genomes]
rs11235546	0.87[ASN][1000 genomes]
rs11235551	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs11605051	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146545	0.80[JPT][hapmap]
rs12797791	0.83[JPT][hapmap]
rs1391888	0.80[JPT][hapmap]
rs1467135	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168173	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980089	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980090	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280098	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341049	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341086	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.88[ASN][1000 genomes]
rs341088	0.91[ASN][1000 genomes]
rs3781938	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781939	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825009	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs429075	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456405	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs458275	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs458575	0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs4943939	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs56350365	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895571	0.87[ASN][1000 genomes]
rs90409	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs907850	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv1794740	chr11:72021720-72332931	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS 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
2	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
3	esv1832864	chr11:72270965-72389125	Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	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
5	nsv468633	chr11:72281884-72336564	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv468634	chr11:72281884-72336564	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv555406	chr11:72281884-72336564	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	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
9	nsv468635	chr11:72284569-72336564	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv555407	chr11:72284569-72336564	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1135029	MRPL21	cis	cerebellum	SCAN
rs1135029	SUV420H1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72269600-72295200	Weak transcription	Right Atrium	heart
2	chr11:72282800-72295200	Weak transcription	Gastric	stomach
3	chr11:72283000-72292000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:72285000-72292200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:72285000-72296200	Weak transcription	Liver	Liver
6	chr11:72285200-72291400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:72286200-72291400	Strong transcription	Spleen	Spleen
8	chr11:72286800-72291400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:72287000-72289400	Strong transcription	Left Ventricle	heart
10	chr11:72287400-72289400	Strong transcription	Fetal Stomach	stomach
11	chr11:72287400-72290400	Strong transcription	Brain Angular Gyrus	brain
12	chr11:72287400-72293000	Strong transcription	Fetal Muscle Leg	muscle
13	chr11:72287400-72295200	Strong transcription	Brain Hippocampus Middle	brain
14	chr11:72287400-72296600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:72287600-72290000	Strong transcription	Fetal Intestine Small	intestine
16	chr11:72287600-72293000	Strong transcription	Brain Cingulate Gyrus	brain
17	chr11:72287600-72295000	Strong transcription	Adipose Nuclei	Adipose
18	chr11:72287600-72295000	Strong transcription	Right Ventricle	heart
19	chr11:72287800-72290000	Strong transcription	Colon Smooth Muscle	Colon
20	chr11:72287800-72290400	Strong transcription	Brain Anterior Caudate	brain
21	chr11:72287800-72294200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:72287800-72294800	Strong transcription	Fetal Brain Female	brain
23	chr11:72287800-72296400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr11:72288000-72290400	Weak transcription	Fetal Intestine Large	intestine
25	chr11:72288000-72293200	Strong transcription	Brain Germinal Matrix	brain
26	chr11:72288000-72293600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr11:72288400-72289400	ZNF genes & repeats	Lung	lung
28	chr11:72288400-72289400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr11:72288400-72290000	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:72288400-72291200	Weak transcription	HSMMtube	muscle
31	chr11:72289200-72289600	ZNF genes & repeats	Hela-S3	cervix
32	chr11:72289200-72293600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
33	chr11:72289200-72294000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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