Variant report

Variant	rs1681630
Chromosome Location	chr11:47969152-47969153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47964759..47967260-chr11:47968299..47969907,3	K562	blood:
2	chr11:47967425..47969925-chr11:48129768..48132712,2	MCF-7	breast:
3	chr11:47968790..47969517-chr11:48130956..48131704,2	MCF-7	breast:
4	chr11:47967526..47970354-chr11:47971440..47973088,2	K562	blood:
5	chr11:47964249..47967260-chr11:47967441..47970649,3	K562	blood:
6	chr11:47968893..47971295-chr11:47973218..47976334,3	K562	blood:
7	chr11:47967043..47970395-chr11:47999984..48003579,8	MCF-7	breast:
8	chr11:47967141..47970110-chr11:47980010..47981597,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPRJ-1	chr11:47968934-47969181	NONHSAT021290

No data

Variant related genes	Relation type
ENSG00000149177	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10742827	0.80[GIH][hapmap]
rs1227995	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1227996	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1228001	0.89[AFR][1000 genomes]
rs1228024	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1631174	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6485802	0.81[GIH][hapmap];0.85[MEX][hapmap]
rs7114598	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS 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 miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1681630	PSMC3	cis	cerebellum	SCAN
rs1681630	MTCH2	cis	cerebellum	SCAN
rs1681630	MYBPC3	cis	multi-tissue	Pritchard
rs1681630	ACP2	cis	lymphoblastoid	seeQTL
rs1681630	MDK	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47950800-47971800	Weak transcription	Fetal Thymus	thymus
2	chr11:47956800-47970200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr11:47960000-47972400	Weak transcription	Lung	lung
4	chr11:47964000-47972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:47966200-47969800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:47966200-47972200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:47966400-47969200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr11:47966600-47972000	Weak transcription	Dnd41	blood
9	chr11:47966800-47970000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:47967200-47971000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:47967400-47969400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:47967400-47973200	Enhancers	Primary B cells from cord blood	blood
13	chr11:47967400-47974000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr11:47967600-47969200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr11:47967600-47969400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:47967600-47971400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr11:47967800-47969200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:47967800-47969400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:47967800-47969400	Flanking Active TSS	A549	lung
20	chr11:47967800-47969400	Enhancers	HMEC	breast
21	chr11:47967800-47969400	Enhancers	NHEK	skin
22	chr11:47967800-47970000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:47967800-47970400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:47968000-47969200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr11:47968000-47970000	Enhancers	NH-A	brain
26	chr11:47968000-47970600	Enhancers	Stomach Mucosa	stomach
27	chr11:47968200-47969200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr11:47968200-47969200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr11:47968200-47969200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr11:47968200-47969200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr11:47968200-47969200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr11:47968200-47969200	Enhancers	HSMM	muscle
33	chr11:47968200-47969200	Enhancers	HUVEC	blood vessel
34	chr11:47968200-47969200	Flanking Active TSS	K562	blood
35	chr11:47968200-47969200	Enhancers	NHDF-Ad	bronchial
36	chr11:47968200-47969400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:47968200-47969400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr11:47968200-47970000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:47968200-47970000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:47968200-47970000	Enhancers	Adipose Nuclei	Adipose
41	chr11:47968200-47970600	Enhancers	Osteobl	bone
42	chr11:47968400-47969200	Enhancers	Primary hematopoietic stem cells	blood
43	chr11:47968400-47969200	Enhancers	Placenta	Placenta
44	chr11:47968400-47969200	Enhancers	Stomach Smooth Muscle	stomach
45	chr11:47968400-47969200	Enhancers	GM12878-XiMat	blood
46	chr11:47968400-47969800	Weak transcription	Primary T cells from cord blood	blood
47	chr11:47968400-47973000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:47968400-47973200	Enhancers	Primary B cells from peripheral blood	blood
49	chr11:47968600-47969200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:47968600-47969200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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