Variant report

Variant	rs546156
Chromosome Location	chr11:75320668-75320669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75307676..75310084-chr11:75318622..75321898,3	MCF-7	breast:
2	chr11:75318925..75322837-chr11:75335237..75336963,3	K562	blood:
3	chr11:75320436..75322582-chr11:75325180..75328802,3	K562	blood:
4	chr11:75318249..75321845-chr11:75322154..75325237,3	MCF-7	breast:
5	chr11:75318997..75321031-chr11:75326821..75329463,2	K562	blood:
6	chr11:75307708..75310392-chr11:75318661..75320948,2	K562	blood:
7	chr11:75306773..75310392-chr11:75318661..75320974,3	K562	blood:

Variant related genes	Relation type
ENSG00000171533	Chromatin interaction
ENSG00000255434	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1145696	0.91[CEU][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1234668	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2508193	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4944086	0.82[TSI][hapmap]
rs541993	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs544698	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs590550	0.82[TSI][hapmap]
rs604694	0.85[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs641976	0.93[EUR][1000 genomes]
rs652452	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs654949	0.85[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs656007	0.91[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs657639	0.90[CEU][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs660343	0.91[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs663515	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs668378	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs687793	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7110142	0.82[TSI][hapmap]
rs7114999	0.82[TSI][hapmap]
rs7128846	0.85[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7947980	0.82[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs546156	KCTD21	cis	parietal	SCAN
rs546156	ITGB2	trans	lymphoblastoid	seeQTL
rs546156	RAB6A	cis	cerebellum	SCAN
rs546156	RELT	cis	cerebellum	SCAN
rs546156	NUMA1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75295400-75329600	Weak transcription	Aorta	Aorta
2	chr11:75296600-75321000	Weak transcription	Ovary	ovary
3	chr11:75305000-75328800	Weak transcription	Pancreas	Pancrea
4	chr11:75305800-75346200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr11:75306000-75326200	Weak transcription	Brain Hippocampus Middle	brain
6	chr11:75306000-75326200	Weak transcription	Brain Substantia Nigra	brain
7	chr11:75306400-75323600	Weak transcription	Spleen	Spleen
8	chr11:75306600-75324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:75309200-75320800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:75310200-75329800	Weak transcription	Fetal Intestine Small	intestine
11	chr11:75311600-75324000	Weak transcription	Right Atrium	heart
12	chr11:75313800-75326000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:75314000-75328000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:75315200-75324400	Weak transcription	Right Ventricle	heart
15	chr11:75316000-75326200	Weak transcription	Fetal Brain Male	brain
16	chr11:75317600-75324000	Weak transcription	Lung	lung
17	chr11:75317600-75346200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:75318000-75326000	Weak transcription	Brain Germinal Matrix	brain
19	chr11:75318400-75326400	Weak transcription	Brain Angular Gyrus	brain
20	chr11:75319200-75321400	Weak transcription	Brain Anterior Caudate	brain
21	chr11:75319200-75325000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr11:75319200-75326000	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:75319400-75321600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr11:75319400-75324400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:75319600-75320800	Enhancers	Fetal Lung	lung
26	chr11:75319600-75321400	Weak transcription	Fetal Brain Female	brain
27	chr11:75319600-75324400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:75319600-75324400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:75319600-75329600	Weak transcription	Fetal Stomach	stomach
30	chr11:75320000-75320800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:75320200-75324200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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