Variant report

Variant	rs7540514
Chromosome Location	chr1:75233608-75233609
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:75230355..75233919-chr1:75236315..75238196,3	K562	blood:
2	chr1:75197358..75200500-chr1:75231674..75234194,4	K562	blood:
3	chr1:75228741..75231063-chr1:75233149..75235215,2	K562	blood:
4	chr1:75226788..75230241-chr1:75231524..75234649,3	K562	blood:

Variant related genes	Relation type
ENSG00000116791	Chromatin interaction
ENSG00000162623	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11162945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1122338	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1133891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11485264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11485299	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12034724	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043726	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13375787	0.85[CHB][hapmap]
rs1359750	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581870	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032969	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs28374065	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445096	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515016	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28563168	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28575168	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28719150	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28740807	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28804147	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28810187	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806161	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650005	0.84[AMR][1000 genomes]
rs4650007	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4650287	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4650288	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58715708	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60292279	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681874	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535692	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768223	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9647	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7540514	TYW3	cis	Artery Tibial	GTEx
rs7540514	TYW3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75216000-75235200	Weak transcription	Right Ventricle	heart
2	chr1:75221400-75238000	Weak transcription	A549	lung
3	chr1:75221600-75234600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:75221600-75237600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:75222200-75236000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:75223000-75235200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:75223600-75235200	Weak transcription	Spleen	Spleen
8	chr1:75225000-75235000	Weak transcription	Fetal Kidney	kidney
9	chr1:75226000-75237600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:75227800-75235600	Weak transcription	HUVEC	blood vessel
11	chr1:75228000-75234400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:75228000-75235200	Weak transcription	Left Ventricle	heart
13	chr1:75228000-75235800	Weak transcription	Aorta	Aorta
14	chr1:75228400-75235000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:75228600-75234200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:75228800-75234600	Weak transcription	HMEC	breast
17	chr1:75230000-75234400	Weak transcription	NH-A	brain
18	chr1:75230200-75234800	Weak transcription	GM12878-XiMat	blood
19	chr1:75230800-75238400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:75231000-75234600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:75231200-75233800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:75231200-75234000	Weak transcription	Adipose Nuclei	Adipose
23	chr1:75231200-75234000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:75231200-75234200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:75231200-75234200	Weak transcription	Brain Anterior Caudate	brain
26	chr1:75231200-75234200	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:75231200-75234200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:75231200-75234400	Weak transcription	Fetal Heart	heart
29	chr1:75231200-75234600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:75231200-75234600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:75231200-75235200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:75231200-75235600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:75231200-75235800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:75231200-75237600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:75231200-75237600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:75231200-75237800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:75231200-75245600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:75231200-75246000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:75231400-75233800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:75231400-75234600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:75231400-75234800	Weak transcription	HSMMtube	muscle
42	chr1:75231600-75236200	Weak transcription	Primary B cells from cord blood	blood
43	chr1:75231800-75235000	Weak transcription	Dnd41	blood
44	chr1:75231800-75235800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:75231800-75237000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:75231800-75237400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:75232000-75234400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:75232000-75234600	Weak transcription	HSMM	muscle
49	chr1:75232200-75238000	Weak transcription	Liver	Liver
50	chr1:75232600-75235000	Weak transcription	Primary T cells from cord blood	blood

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