Variant report

Variant	rs2155340
Chromosome Location	chr11:105959082-105959083
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:105958384-105959093	A549	lung:	n/a	n/a
2	RAD21	chr11:105958489-105959095	MCF-7	breast:	n/a	n/a
3	CTCF	chr11:105958078-105959116	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr11:105958354-105959717	SK-N-SH	brain:	n/a	n/a
5	SMC3	chr11:105958534-105959132	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr11:105958310-105959283	IMR90	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:105947111..105951134-chr11:105957312..105961780,4	MCF-7	breast:
2	chr11:105957718..105960222-chr11:105960868..105964221,4	K562	blood:
3	chr11:105958412..105959145-chr11:106004183..106004754,2	MCF-7	breast:
4	chr11:105958730..105959235-chr11:106907710..106908538,2	K562	blood:
5	chr11:105947180..105950482-chr11:105957970..105961009,3	K562	blood:

No data

Variant related genes	Relation type
AASDHPPT	TF binding region
ENSG00000182359	Chromatin interaction
ENSG00000149313	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10791780	0.85[CHB][hapmap]
rs10895899	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895900	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap]
rs10895904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226915	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11226922	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11226931	0.83[ASN][1000 genomes]
rs12365489	0.85[CHB][hapmap]
rs17105049	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs1893174	0.95[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1939798	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1939799	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1940772	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2186731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3740869	0.85[CHB][hapmap]
rs4237618	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4440991	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4474407	0.85[CHB][hapmap]
rs4485076	0.81[EUR][1000 genomes]
rs4565867	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4754141	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7130759	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131047	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754562	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs7554	0.85[CHB][hapmap]
rs766717	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs9651674	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9943677	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1048381	chr11:105945117-106561574	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2155340	KDELC2	cis	cerebellum	SCAN
rs2155340	AASDHPPT	cis	lymphoblastoid	seeQTL
rs2155340	AASDHPPT	cis	multi-tissue	Pritchard
rs2155340	MMP12	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105949000-105973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:105949200-105962200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:105949200-105966000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:105949200-105967800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:105949200-105969800	Weak transcription	Lung	lung
6	chr11:105949200-105971600	Weak transcription	Esophagus	oesophagus
7	chr11:105949800-105962200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:105949800-105962200	Weak transcription	Thymus	Thymus
9	chr11:105950400-105971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:105950600-105969400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:105951200-105962200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:105952000-105969400	Weak transcription	Colonic Mucosa	Colon
13	chr11:105953000-105961800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:105953200-105960400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:105953400-105962000	Weak transcription	Placenta	Placenta
16	chr11:105953400-105962200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:105953400-105962400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:105953400-105962400	Weak transcription	Ovary	ovary
19	chr11:105953400-105962400	Weak transcription	Right Ventricle	heart
20	chr11:105953400-105965600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:105953400-105970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:105953600-105969600	Weak transcription	Gastric	stomach
23	chr11:105954000-105959600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:105954000-105961600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:105954000-105962000	Weak transcription	HMEC	breast
26	chr11:105954000-105962400	Weak transcription	HSMMtube	muscle
27	chr11:105954000-105963000	Weak transcription	NHDF-Ad	bronchial
28	chr11:105954200-105959400	Weak transcription	NH-A	brain
29	chr11:105954200-105961800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:105954400-105961000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:105954400-105961600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:105955000-105959400	Weak transcription	NHEK	skin
33	chr11:105955400-105962400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:105956000-105970000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:105956200-105959200	Genic enhancers	Dnd41	blood
36	chr11:105956200-105959600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr11:105956200-105959800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:105956200-105960400	Strong transcription	HSMM	muscle
39	chr11:105956200-105962200	Weak transcription	Fetal Stomach	stomach
40	chr11:105956400-105961400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:105956400-105961400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr11:105956600-105960000	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr11:105956800-105959200	Enhancers	Fetal Brain Female	brain
44	chr11:105956800-105959200	Enhancers	NHLF	lung
45	chr11:105956800-105959600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:105956800-105960200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr11:105956800-105960600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:105956800-105962400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr11:105957000-105959800	Enhancers	Colon Smooth Muscle	Colon
50	chr11:105957000-105960200	Enhancers	Osteobl	bone

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