Variant report

Variant	rs12787554
Chromosome Location	chr11:8668569-8668570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8666699..8668669-chr11:8675245..8676830,2	K562	blood:
2	chr11:8653441..8656999-chr11:8666272..8669350,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10160373	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1026021	1.00[MEX][hapmap]
rs10743073	0.95[MEX][hapmap]
rs10743084	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840102	0.88[AFR][1000 genomes]
rs10840104	0.86[AFR][1000 genomes]
rs11042019	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042030	0.91[AFR][1000 genomes]
rs11042033	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12286011	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12295729	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12295855	0.89[MEX][hapmap]
rs13328833	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16938253	0.90[MEX][hapmap]
rs2166470	0.90[MEX][hapmap]
rs34655699	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35319120	0.90[AFR][1000 genomes]
rs3942866	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57012665	0.86[ASN][1000 genomes]
rs7110529	0.92[AFR][1000 genomes]
rs7118611	0.86[AFR][1000 genomes]
rs7931834	0.95[MEX][hapmap]
rs7935453	0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs7941510	0.88[AFR][1000 genomes]
rs7947230	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][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	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12787554	HBB	cis	cerebellum	SCAN
rs12787554	SNORA45	cis	cerebellum	SCAN
rs12787554	RPL27A	cis	parietal	SCAN
rs12787554	AMPD3	cis	parietal	SCAN
rs12787554	RPL27A	cis	cerebellum	SCAN
rs12787554	SWAP70	cis	cerebellum	SCAN
rs12787554	STK33	cis	cerebellum	SCAN
rs12787554	OR51E2	cis	cerebellum	SCAN
rs12787554	SNORA45	cis	parietal	SCAN
rs12787554	OR52E2	cis	parietal	SCAN
rs12787554	ST5	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8637000-8703200	Weak transcription	Small Intestine	intestine
2	chr11:8646200-8671000	Weak transcription	HUVEC	blood vessel
3	chr11:8650800-8676200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:8652200-8675000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr11:8654000-8673800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr11:8654200-8673800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr11:8654200-8675600	Strong transcription	Stomach Smooth Muscle	stomach
8	chr11:8654400-8672400	Strong transcription	Brain Anterior Caudate	brain
9	chr11:8655000-8670200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:8655000-8676400	Strong transcription	Primary T cells from cord blood	blood
11	chr11:8655200-8672600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:8655400-8673400	Strong transcription	Dnd41	blood
13	chr11:8655600-8670600	Strong transcription	Adipose Nuclei	Adipose
14	chr11:8656000-8670600	Strong transcription	Fetal Muscle Leg	muscle
15	chr11:8656000-8672600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:8656000-8672800	Strong transcription	Placenta	Placenta
17	chr11:8656600-8671600	Strong transcription	Brain Cingulate Gyrus	brain
18	chr11:8657200-8673800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:8657400-8672600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:8658000-8675200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:8658200-8672400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:8658200-8673800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr11:8658400-8671200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr11:8658400-8671600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:8658600-8673000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:8658600-8674200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:8658600-8675000	Strong transcription	Liver	Liver
28	chr11:8659200-8670400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:8659200-8673600	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:8659400-8669000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:8660000-8669200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:8660200-8671000	Weak transcription	NHDF-Ad	bronchial
33	chr11:8660400-8669200	Weak transcription	Colonic Mucosa	Colon
34	chr11:8660400-8670200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:8660800-8670800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:8661800-8673600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr11:8662400-8669800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:8662400-8670200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr11:8662600-8669000	Weak transcription	Right Ventricle	heart
40	chr11:8662600-8680200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:8662600-8692000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:8662800-8671200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:8662800-8675400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr11:8663000-8668800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:8663000-8671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr11:8663000-8671000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:8663000-8680200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:8663200-8670000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:8663200-8680000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr11:8663400-8670200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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