Variant report

Variant	rs11550057
Chromosome Location	chr11:66392880-66392881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89621652..89622207-chr11:66392595..66393095,2	Hela-S3	cervix:
2	chr11:66372340..66374886-chr11:66390314..66393564,3	K562	blood:
3	chr11:66390889..66393382-chr8:48648876..48650745,2	MCF-7	breast:
4	chr11:66085300..66087930-chr11:66392771..66394430,2	K562	blood:
5	chr11:66359839..66362729-chr11:66392141..66393902,2	MCF-7	breast:
6	chr11:66327944..66330725-chr11:66391381..66393880,2	K562	blood:
7	chr11:66356872..66361131-chr11:66390799..66394661,4	K562	blood:

Variant related genes	Relation type
ENSG00000182791	Chromatin interaction
ENSG00000173992	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10896128	0.81[EUR][1000 genomes]
rs1127145	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs15969	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17495838	1.00[LWK][hapmap]
rs17496250	1.00[YRI][hapmap]
rs2229456	0.85[CEU][hapmap]
rs2275998	0.85[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs3816492	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3867132	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3867133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519380	0.84[TSI][hapmap]
rs57043177	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57127845	0.81[EUR][1000 genomes]
rs59320108	0.82[EUR][1000 genomes]
rs59431265	0.81[EUR][1000 genomes]
rs59566349	0.81[EUR][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	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11550057	ESRRA	cis	cerebellum	SCAN
rs11550057	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs11550057	CCND1	cis	parietal	SCAN
rs11550057	PACS1	cis	parietal	SCAN
rs11550057	COX8A	cis	cerebellum	SCAN
rs11550057	UNC93B1	cis	cerebellum	SCAN
rs11550057	CTSF	cis	parietal	SCAN
rs11550057	CCS	cis	cerebellum	SCAN
rs11550057	SPTBN2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66385400-66406200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66386200-66398400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr11:66386800-66393200	Weak transcription	HSMMtube	muscle
4	chr11:66386800-66393400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:66386800-66405600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:66387000-66393600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:66387000-66403400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:66387600-66397000	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr11:66387600-66401800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:66388400-66398000	Strong transcription	NHEK	skin
11	chr11:66388600-66398200	Strong transcription	Primary hematopoietic stem cells	blood
12	chr11:66388600-66398400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:66388600-66402400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:66388800-66398000	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr11:66388800-66398000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:66388800-66398400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:66388800-66399800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:66388800-66401200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:66388800-66402400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:66388800-66402400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr11:66388800-66402400	Strong transcription	Fetal Muscle Leg	muscle
22	chr11:66388800-66402800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:66388800-66403800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:66388800-66404400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:66388800-66404800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:66389000-66393600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr11:66389000-66404400	Strong transcription	Fetal Thymus	thymus
28	chr11:66389200-66398600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:66389200-66402400	Strong transcription	Fetal Intestine Large	intestine
30	chr11:66389200-66402800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:66389800-66393200	Genic enhancers	Pancreas	Pancrea
32	chr11:66389800-66393600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr11:66389800-66395200	Genic enhancers	Adipose Nuclei	Adipose
34	chr11:66389800-66398400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:66389800-66401200	Strong transcription	Thymus	Thymus
36	chr11:66390000-66393600	Genic enhancers	Brain Angular Gyrus	brain
37	chr11:66390000-66394400	Genic enhancers	Brain Inferior Temporal Lobe	brain
38	chr11:66390000-66398000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:66390200-66397800	Strong transcription	NHDF-Ad	bronchial
40	chr11:66390200-66398200	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr11:66390200-66398400	Strong transcription	Fetal Brain Female	brain
42	chr11:66390200-66401200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:66390400-66393600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr11:66390400-66397800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:66390400-66398000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr11:66390400-66398000	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr11:66390400-66398200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:66390400-66398400	Strong transcription	Brain Germinal Matrix	brain
49	chr11:66390600-66393000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr11:66390600-66393600	Genic enhancers	Spleen	Spleen

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