Variant report

Variant	rs11937178
Chromosome Location	chr4:148847599-148847600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10049932	0.81[MEX][hapmap]
rs10519921	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11934409	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	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941546	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11942547	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11946732	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes]
rs13434578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435747	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024137	0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17024143	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17614013	1.00[TSI][hapmap]
rs187006	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2118033	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2118035	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164530	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2164531	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2358180	0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2358181	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2635256	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2635266	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2635267	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2635268	0.86[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4027114	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4027115	1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs4337713	0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs55752555	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs67913037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72617450	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7655265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669783	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7672161	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7685779	0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs975371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975372	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs11937178	DEFB119	trans	brain	seeQTL
rs11937178	GSG1	trans	brain	seeQTL
rs11937178	SH2D2A	trans	brain	seeQTL
rs11937178	ENO3	trans	brain	seeQTL
rs11937178	ROR1	trans	brain	seeQTL
rs11937178	CRX	trans	brain	seeQTL
rs11937178	TTR	trans	brain	seeQTL
rs11937178	GNB3	trans	brain	seeQTL
rs11937178	LRTM1	trans	brain	seeQTL
rs11937178	SLC5A7	trans	brain	seeQTL
rs11937178	OTX2	trans	brain	seeQTL
rs11937178	GUCA1C	trans	brain	seeQTL
rs11937178	PDE6H	trans	brain	seeQTL

Chromatin state (count:66 , 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	chr4:148820800-148848800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:148824400-148854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:148824600-148854400	Weak transcription	Right Ventricle	heart
10	chr4:148825200-148848400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:148825400-148861200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:148825400-148865800	Weak transcription	Fetal Lung	lung
13	chr4:148826600-148888200	Weak transcription	Fetal Thymus	thymus
14	chr4:148827400-148861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:148829400-148864200	Weak transcription	Primary T cells from cord blood	blood
16	chr4:148831600-148849000	Weak transcription	NH-A	brain
17	chr4:148832200-148848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:148832200-148854400	Weak transcription	NHEK	skin
19	chr4:148833600-148848400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:148833600-148877400	Weak transcription	Small Intestine	intestine
21	chr4:148834800-148849000	Weak transcription	NHLF	lung
22	chr4:148834800-148861400	Weak transcription	Fetal Intestine Large	intestine
23	chr4:148835000-148867200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:148835000-148869000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:148835600-148848800	Weak transcription	Fetal Stomach	stomach
26	chr4:148835600-148854400	Weak transcription	Fetal Intestine Small	intestine
27	chr4:148836400-148848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:148836400-148861000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:148836600-148867000	Weak transcription	HMEC	breast
30	chr4:148837600-148850600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:148837800-148854400	Weak transcription	Left Ventricle	heart
32	chr4:148838400-148848400	Weak transcription	HUVEC	blood vessel
33	chr4:148838400-148848800	Weak transcription	NHDF-Ad	bronchial
34	chr4:148838400-148858400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:148838600-148848200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:148838600-148848800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:148838800-148849400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:148838800-148854400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:148840200-148853000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:148843000-148848800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:148843400-148848000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:148843400-148848400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:148843400-148848400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:148843400-148848400	Weak transcription	Aorta	Aorta
45	chr4:148843400-148848400	Weak transcription	Ovary	ovary
46	chr4:148843400-148848800	Weak transcription	Lung	lung
47	chr4:148843400-148854400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:148843400-148854400	Weak transcription	HSMMtube	muscle
49	chr4:148843600-148848400	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:148843600-148848400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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