Variant report

Variant	rs978534
Chromosome Location	chr4:124749377-124749378
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1016592	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129313	1.00[CEU][hapmap]
rs1991839	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2390590	0.86[ASN][1000 genomes]
rs3097909	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3097910	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3097913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097915	0.88[EUR][1000 genomes]
rs3097916	0.88[EUR][1000 genomes]
rs3097917	0.92[EUR][1000 genomes]
rs3097918	0.92[EUR][1000 genomes]
rs3097919	0.84[EUR][1000 genomes]
rs3097920	0.89[EUR][1000 genomes]
rs3113385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113396	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs6840618	1.00[CEU][hapmap]
rs721456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654237	1.00[CEU][hapmap]
rs7699221	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2754745	chr4:124698055-124770865	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs978534	TNIP3	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124735200-124753800	Weak transcription	Psoas Muscle	Psoas
2	chr4:124737600-124752200	Weak transcription	Gastric	stomach
3	chr4:124743200-124759800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:124743600-124751000	Weak transcription	Fetal Lung	lung
5	chr4:124743800-124752000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:124743800-124752600	Weak transcription	Right Atrium	heart
7	chr4:124744000-124752400	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:124746400-124750600	Weak transcription	Fetal Intestine Large	intestine
9	chr4:124746600-124750200	Weak transcription	Fetal Intestine Small	intestine
10	chr4:124747000-124753200	Weak transcription	Aorta	Aorta
11	chr4:124747400-124749400	Enhancers	Fetal Heart	heart
12	chr4:124747400-124752600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:124747400-124752800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:124747600-124750800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:124747600-124752200	Weak transcription	Fetal Stomach	stomach
16	chr4:124747600-124752600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:124747600-124752800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:124748000-124749400	Enhancers	HUVEC	blood vessel
19	chr4:124748200-124752200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:124748400-124753400	Weak transcription	Ovary	ovary
21	chr4:124748400-124753800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:124748600-124750200	Weak transcription	HMEC	breast
23	chr4:124748600-124750600	Weak transcription	HSMMtube	muscle
24	chr4:124748600-124750800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:124748600-124750800	Weak transcription	NH-A	brain
26	chr4:124748600-124752400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:124748600-124752400	Weak transcription	Osteobl	bone
28	chr4:124749000-124750200	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:124749000-124750200	Weak transcription	NHLF	lung
30	chr4:124749000-124750800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:124749000-124751200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:124749000-124751400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:124749000-124752000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:124749000-124752000	Weak transcription	HSMM	muscle
35	chr4:124749000-124752200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:124749200-124750600	Weak transcription	NHDF-Ad	bronchial
37	chr4:124749200-124752000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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