Variant report

Variant	rs1557765
Chromosome Location	chr11:17403639-17403640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17401527..17405179-chr11:17405771..17408702,5	K562	blood:
2	chr11:17403171..17405241-chr11:17406430..17408298,2	MCF-7	breast:
3	chr11:17403459..17406167-chr11:17526057..17528257,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP1-239B22.1.1-1	chr11:17402196-17405078	ENSG00000260196.1
2	lnc-RP1-239B22.1.1-1	chr11:17402953-17405078	NONHSAT018230

Variant related genes	Relation type
ENSG00000187486	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1002226	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10734252	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766392	0.85[CHB][hapmap]
rs10832776	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832778	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024268	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024271	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12146443	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12146652	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2051772	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074310	0.81[EUR][1000 genomes]
rs2074311	0.81[CHB][hapmap]
rs2074314	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4148646	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4439492	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5213	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5215	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5219	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7124355	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7484027	0.85[CHB][hapmap]
rs757110	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7928810	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv467712	chr11:17393644-17418477	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv553583	chr11:17393644-17418477	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv517772	chr11:17401134-17427862	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv897018	chr11:17403639-17417337	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv528959	chr11:17403639-17435214	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Social communication problems	24564958	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1557765	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs1557765	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs1557765	TSG101	cis	cerebellum	SCAN
rs1557765	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs1557765	SAA4	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17394200-17407600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:17394400-17405000	Weak transcription	Brain Angular Gyrus	brain
3	chr11:17394400-17410200	Weak transcription	A549	lung
4	chr11:17395200-17405200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:17395200-17405800	Weak transcription	Gastric	stomach
6	chr11:17395200-17410200	Weak transcription	Thymus	Thymus
7	chr11:17395600-17406200	Weak transcription	Pancreas	Pancrea
8	chr11:17395600-17410200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:17395600-17410400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:17395800-17405200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr11:17395800-17405400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:17395800-17405400	Weak transcription	Left Ventricle	heart
13	chr11:17395800-17409200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:17396000-17408800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:17396600-17404600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr11:17396600-17410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:17397200-17404800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:17397200-17407800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:17398200-17410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:17398400-17405400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr11:17398800-17410200	Weak transcription	Primary T cells from cord blood	blood
22	chr11:17399000-17404600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr11:17399200-17404200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:17400600-17404200	Weak transcription	Ovary	ovary
25	chr11:17400600-17408000	Strong transcription	Fetal Intestine Small	intestine
26	chr11:17400600-17408800	Weak transcription	Brain Germinal Matrix	brain
27	chr11:17400800-17403800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:17400800-17407200	Weak transcription	Fetal Brain Female	brain
29	chr11:17400800-17410200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:17401000-17405600	Weak transcription	Brain Hippocampus Middle	brain
31	chr11:17401000-17410200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:17401200-17404600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:17401200-17405200	Weak transcription	Brain Anterior Caudate	brain
34	chr11:17401200-17405400	Weak transcription	Psoas Muscle	Psoas
35	chr11:17401200-17407200	Weak transcription	Lung	lung
36	chr11:17401600-17405200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:17401600-17405200	Strong transcription	Dnd41	blood
38	chr11:17401600-17410200	Weak transcription	Hela-S3	cervix
39	chr11:17401600-17410200	Weak transcription	K562	blood
40	chr11:17401800-17404000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:17401800-17405200	Weak transcription	NHEK	skin
42	chr11:17401800-17405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:17401800-17405600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:17401800-17407400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:17401800-17407400	Weak transcription	HepG2	liver
46	chr11:17401800-17410200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr11:17402000-17404800	Weak transcription	Fetal Muscle Leg	muscle
48	chr11:17402000-17410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr11:17402000-17410200	Weak transcription	HMEC	breast
50	chr11:17402400-17404400	Enhancers	NHDF-Ad	bronchial

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