Variant report

Variant	rs2154754
Chromosome Location	chr11:77178698-77178699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77176359..77179298-chr11:77182598..77185560,4	K562	blood:
2	chr11:77177499..77180436-chr11:77182683..77185678,3	K562	blood:

Variant related genes	Relation type
ENSG00000149269	Chromatin interaction
ENSG00000268635	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11237190	0.81[ASN][1000 genomes]
rs11237200	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11820118	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11828786	0.94[JPT][hapmap]
rs1237490	0.88[ASN][1000 genomes]
rs12420360	0.93[JPT][hapmap]
rs17135689	0.81[ASN][1000 genomes]
rs2602471	0.94[JPT][hapmap]
rs2602473	0.94[JPT][hapmap]
rs2602474	0.94[JPT][hapmap]
rs2602475	0.94[JPT][hapmap]
rs2602476	0.86[EUR][1000 genomes]
rs2602481	0.89[JPT][hapmap]
rs2602482	0.89[JPT][hapmap]
rs2725829	0.94[JPT][hapmap]
rs2729756	0.94[JPT][hapmap]
rs2729772	0.83[JPT][hapmap]
rs2729775	0.92[JPT][hapmap]
rs2844327	0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2852388	0.94[JPT][hapmap]
rs2852390	0.94[JPT][hapmap]
rs2853085	0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2853095	0.94[JPT][hapmap]
rs2853098	0.89[JPT][hapmap]
rs2888377	0.94[JPT][hapmap]
rs3015982	0.86[EUR][1000 genomes]
rs3015983	0.88[EUR][1000 genomes]
rs3015985	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs3015986	0.88[EUR][1000 genomes]
rs3015988	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs3015990	0.89[EUR][1000 genomes]
rs3015992	0.93[EUR][1000 genomes]
rs3019233	0.87[EUR][1000 genomes]
rs3019234	0.87[EUR][1000 genomes]
rs3019235	0.87[EUR][1000 genomes]
rs3019236	0.87[EUR][1000 genomes]
rs3019249	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019257	0.88[EUR][1000 genomes]
rs34025917	0.88[EUR][1000 genomes]
rs4092275	0.81[ASN][1000 genomes]
rs472691	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs476258	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs479104	0.86[EUR][1000 genomes]
rs493256	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs4944160	0.81[ASN][1000 genomes]
rs503406	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs505841	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs508662	0.83[EUR][1000 genomes]
rs522015	0.81[EUR][1000 genomes]
rs523481	0.83[EUR][1000 genomes]
rs531638	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535008	0.84[EUR][1000 genomes]
rs552323	0.83[EUR][1000 genomes]
rs557484	0.82[EUR][1000 genomes]
rs558470	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs560571	0.86[EUR][1000 genomes]
rs561386	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs562845	0.84[EUR][1000 genomes]
rs563731	0.84[EUR][1000 genomes]
rs572485	0.83[EUR][1000 genomes]
rs57305199	0.81[ASN][1000 genomes]
rs576220	0.81[EUR][1000 genomes]
rs580624	0.83[EUR][1000 genomes]
rs595654	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs644551	0.83[EUR][1000 genomes]
rs649040	0.83[EUR][1000 genomes]
rs674259	0.80[EUR][1000 genomes]
rs683455	0.85[EUR][1000 genomes]
rs683762	0.83[EUR][1000 genomes]
rs684793	0.85[EUR][1000 genomes]
rs689108	0.86[EUR][1000 genomes]
rs733358	0.89[JPT][hapmap]
rs7934230	0.89[EUR][1000 genomes]
rs7949721	0.88[EUR][1000 genomes]
rs876319	0.94[JPT][hapmap]
rs947809	0.81[ASN][1000 genomes]
rs947810	0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2154754	PAK1	cis	parietal	SCAN
rs2154754	UCP2	cis	cerebellum	SCAN
rs2154754	KCTD14	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77155400-77181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:77161200-77179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:77167800-77182000	Weak transcription	Fetal Kidney	kidney
4	chr11:77168600-77178800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr11:77168800-77179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr11:77169000-77181400	Weak transcription	Brain Angular Gyrus	brain
7	chr11:77170800-77179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:77171200-77181600	Weak transcription	Primary B cells from cord blood	blood
9	chr11:77173800-77183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:77174600-77180400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr11:77174800-77179000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:77175000-77179000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr11:77175400-77179200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:77175400-77181400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:77175600-77178800	Weak transcription	Fetal Intestine Small	intestine
16	chr11:77175800-77179400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:77177200-77180200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr11:77177800-77180000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr11:77177800-77180200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr11:77177800-77180400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr11:77178000-77179200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:77178000-77180000	Enhancers	Stomach Mucosa	stomach
23	chr11:77178000-77180400	Enhancers	Small Intestine	intestine
24	chr11:77178000-77181400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:77178200-77178800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr11:77178200-77179800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:77178200-77180000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr11:77178200-77180600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:77178200-77181000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr11:77178200-77181200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr11:77178200-77181200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr11:77178200-77181400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:77178200-77181400	Enhancers	Duodenum Mucosa	Duodenum
34	chr11:77178200-77181400	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr11:77178200-77182800	Enhancers	Fetal Intestine Large	intestine
36	chr11:77178400-77179400	Active TSS	GM12878-XiMat	blood
37	chr11:77178400-77179400	Enhancers	Hela-S3	cervix
38	chr11:77178400-77181400	Weak transcription	Colonic Mucosa	Colon
39	chr11:77178400-77182000	Weak transcription	Fetal Brain Male	brain
40	chr11:77178400-77182400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:77178400-77183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:77178400-77183400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:77178600-77179200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:77178600-77179200	Enhancers	Psoas Muscle	Psoas

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