Variant report

Variant	rs2245735
Chromosome Location	chr4:159049020-159049021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10517684	0.90[CEU][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap]
rs10517688	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs10857307	0.95[CEU][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap]
rs10857308	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs12504989	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs12506818	0.82[EUR][1000 genomes]
rs12506953	0.82[EUR][1000 genomes]
rs12511578	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12650454	0.90[CEU][hapmap]
rs17036918	0.90[CEU][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap]
rs17036921	0.89[CHD][hapmap];0.87[JPT][hapmap]
rs17037003	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17037241	0.84[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs4129400	0.90[CEU][hapmap];0.87[JPT][hapmap]
rs4398571	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4460050	0.95[CEU][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap]
rs4691449	0.95[CEU][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap]
rs62335861	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62335862	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62337014	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62337015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6536298	0.85[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs6814979	0.93[JPT][hapmap]
rs7384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7692254	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv880293	chr4:159012365-159049020	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2245735	GDI2	trans	parietal	SCAN
rs2245735	FAM198B	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042200-159051400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:159042400-159050800	Weak transcription	Aorta	Aorta
3	chr4:159042600-159053400	Weak transcription	Right Atrium	heart
4	chr4:159042600-159053600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain
6	chr4:159042800-159050000	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:159042800-159053400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:159042800-159053800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:159042800-159054800	Weak transcription	Fetal Heart	heart
10	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:159043200-159051200	Weak transcription	Left Ventricle	heart
12	chr4:159043800-159051400	Weak transcription	Fetal Stomach	stomach
13	chr4:159044000-159049800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:159044200-159052200	Weak transcription	Osteobl	bone
15	chr4:159044400-159051800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:159044600-159050600	Weak transcription	NHDF-Ad	bronchial
17	chr4:159044600-159050800	Weak transcription	NHLF	lung
18	chr4:159044600-159051000	Weak transcription	HSMMtube	muscle
19	chr4:159044800-159071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:159045200-159058600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:159045200-159059400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:159045400-159050800	Strong transcription	HSMM	muscle
24	chr4:159045800-159052000	Weak transcription	Fetal Intestine Small	intestine
25	chr4:159046200-159054200	Strong transcription	HUVEC	blood vessel
26	chr4:159046400-159053400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:159046600-159049600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:159046800-159050800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:159046800-159053200	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:159047000-159049600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:159047000-159051200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
33	chr4:159047200-159049400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:159047200-159052000	Strong transcription	Adipose Nuclei	Adipose
35	chr4:159047200-159058600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:159047400-159049200	Strong transcription	HMEC	breast
37	chr4:159048000-159049600	Weak transcription	Stomach Mucosa	stomach
38	chr4:159048000-159051800	Strong transcription	Fetal Intestine Large	intestine
39	chr4:159048800-159051400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:159049000-159049400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:159049000-159049800	Weak transcription	HepG2	liver
42	chr4:159049000-159050600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:159049000-159050800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:159049000-159052200	Strong transcription	Ovary	ovary

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