Variant report

Variant	rs11934409
Chromosome Location	chr4:148848885-148848886
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11937178	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11939997	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11941546	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11942547	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11946732	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13434578	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13435747	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17024137	0.89[EUR][1000 genomes]
rs17024143	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs187006	0.86[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs2118033	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs2118035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2164530	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2164531	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2358180	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2358181	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2635256	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs2635266	0.86[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs2635267	0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2635268	0.86[CHB][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap]
rs4027114	0.89[EUR][1000 genomes]
rs4337713	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs55752555	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67913037	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72617450	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7655265	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7666206	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7669783	0.95[CHB][hapmap]
rs7672161	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs975371	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs975372	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1024596	chr4:148830472-148886915	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11934409	LRTM1	trans	brain	seeQTL
rs11934409	GNB3	trans	brain	seeQTL
rs11934409	GUCA1C	trans	brain	seeQTL
rs11934409	TTR	trans	brain	seeQTL
rs11934409	DEFB119	trans	brain	seeQTL
rs11934409	GSG1	trans	brain	seeQTL
rs11934409	ROR1	trans	brain	seeQTL
rs11934409	PDE6H	trans	brain	seeQTL
rs11934409	SLC5A7	trans	brain	seeQTL
rs11934409	SH2D2A	trans	brain	seeQTL
rs11934409	OTX2	trans	brain	seeQTL
rs11934409	CRX	trans	brain	seeQTL
rs11934409	ENO3	trans	brain	seeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
2	chr4:148796800-148863200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:148796800-148866000	Weak transcription	Thymus	Thymus
4	chr4:148797400-148879600	Weak transcription	Gastric	stomach
5	chr4:148804600-148854400	Weak transcription	Psoas Muscle	Psoas
6	chr4:148820600-148861200	Weak transcription	Esophagus	oesophagus
7	chr4:148824400-148854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:148824600-148854400	Weak transcription	Right Ventricle	heart
9	chr4:148825400-148861200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:148825400-148865800	Weak transcription	Fetal Lung	lung
11	chr4:148826600-148888200	Weak transcription	Fetal Thymus	thymus
12	chr4:148827400-148861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:148829400-148864200	Weak transcription	Primary T cells from cord blood	blood
14	chr4:148831600-148849000	Weak transcription	NH-A	brain
15	chr4:148832200-148854400	Weak transcription	NHEK	skin
16	chr4:148833600-148877400	Weak transcription	Small Intestine	intestine
17	chr4:148834800-148849000	Weak transcription	NHLF	lung
18	chr4:148834800-148861400	Weak transcription	Fetal Intestine Large	intestine
19	chr4:148835000-148867200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:148835000-148869000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:148835600-148854400	Weak transcription	Fetal Intestine Small	intestine
22	chr4:148836400-148861000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:148836600-148867000	Weak transcription	HMEC	breast
24	chr4:148837600-148850600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:148837800-148854400	Weak transcription	Left Ventricle	heart
26	chr4:148838400-148858400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:148838800-148849400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:148838800-148854400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:148840200-148853000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:148843400-148854400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:148843400-148854400	Weak transcription	HSMMtube	muscle
32	chr4:148844600-148850000	Weak transcription	Fetal Brain Male	brain
33	chr4:148846600-148849400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:148846800-148849200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:148846800-148849200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr4:148846800-148853600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:148847000-148854800	Weak transcription	Fetal Kidney	kidney
38	chr4:148847200-148849200	Weak transcription	Stomach Mucosa	stomach
39	chr4:148847200-148849400	Strong transcription	HSMM	muscle
40	chr4:148847400-148877200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:148848000-148849000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:148848000-148849800	Strong transcription	GM12878-XiMat	blood
43	chr4:148848200-148849000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:148848200-148849600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:148848200-148850200	Strong transcription	Adipose Nuclei	Adipose
46	chr4:148848400-148849000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:148848400-148849000	Genic enhancers	Aorta	Aorta
48	chr4:148848400-148849000	Enhancers	Fetal Muscle Leg	muscle
49	chr4:148848400-148849200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:148848400-148849200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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