Variant report

Variant	rs7987701
Chromosome Location	chr13:40137822-40137823
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11618841	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11619569	0.88[ASN][1000 genomes]
rs12428145	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1475177	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17060207	0.87[ASN][1000 genomes]
rs17060285	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2324334	0.87[ASN][1000 genomes]
rs2324336	0.84[JPT][hapmap]
rs2324338	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2324341	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56066871	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59443260	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6563724	0.88[ASN][1000 genomes]
rs6563725	0.88[ASN][1000 genomes]
rs7324765	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73466835	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7992600	0.88[ASN][1000 genomes]
rs7998105	0.81[ASN][1000 genomes]
rs7998772	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8000770	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9594342	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9603561	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9603565	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs967401	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	esv3337679	chr13:40137781-40138289	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7987701	TRPC4	cis	cerebellum	SCAN
rs7987701	FREM2	cis	cerebellum	SCAN
rs7987701	TYMS	trans	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40107800-40140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:40129000-40145600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:40129000-40152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:40130000-40139600	Weak transcription	Fetal Stomach	stomach
5	chr13:40131000-40138600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:40131000-40138600	Weak transcription	Adipose Nuclei	Adipose
7	chr13:40132200-40145600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr13:40133800-40138000	Weak transcription	Aorta	Aorta
9	chr13:40133800-40138200	Weak transcription	Brain Substantia Nigra	brain
10	chr13:40134000-40139400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:40134200-40139800	Weak transcription	Fetal Muscle Leg	muscle
12	chr13:40135400-40138000	Weak transcription	Left Ventricle	heart
13	chr13:40135400-40139600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr13:40135400-40139800	Weak transcription	Right Atrium	heart
15	chr13:40135800-40139200	Enhancers	NHEK	skin
16	chr13:40135800-40139400	Enhancers	HMEC	breast
17	chr13:40135800-40142000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:40135800-40145600	Weak transcription	Lung	lung
19	chr13:40136000-40138600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:40136200-40138600	Enhancers	HSMMtube	muscle
21	chr13:40136200-40138800	Enhancers	NHDF-Ad	bronchial
22	chr13:40136200-40139000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:40136200-40139600	Enhancers	HSMM	muscle
24	chr13:40136400-40145600	Weak transcription	Right Ventricle	heart
25	chr13:40136800-40138800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:40136800-40138800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr13:40136800-40139000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:40136800-40139000	Enhancers	Osteobl	bone
29	chr13:40136800-40140800	Enhancers	Ovary	ovary
30	chr13:40136800-40141200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr13:40137000-40138800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr13:40137000-40139200	Enhancers	NH-A	brain
33	chr13:40137000-40139400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:40137000-40139600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:40137000-40139600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:40137000-40139600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr13:40137000-40140600	Enhancers	Fetal Heart	heart
38	chr13:40137200-40138000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr13:40137200-40138400	Enhancers	NHLF	lung
40	chr13:40137200-40138600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:40137200-40139400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr13:40137400-40138000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr13:40137400-40138800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:40137400-40139200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr13:40137400-40139200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr13:40137600-40138200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr13:40137600-40138200	Enhancers	Fetal Lung	lung
48	chr13:40137600-40138200	Enhancers	Rectal Smooth Muscle	rectum
49	chr13:40137600-40138400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr13:40137600-40139200	Enhancers	Placenta Amnion	Placenta Amnion

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