Variant report

Variant	rs1471750
Chromosome Location	chr4:79301614-79301615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11098160	0.92[ASN][1000 genomes]
rs11098164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11932185	0.92[ASN][1000 genomes]
rs1872264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1872265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100483	0.89[ASN][1000 genomes]
rs4975163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533620	0.92[ASN][1000 genomes]
rs7670150	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923017	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923019	0.85[CHB][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv3443485	chr4:79300628-79303526	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1471750	RCHY1	cis	cerebellum	SCAN
rs1471750	SDAD1	cis	parietal	SCAN
rs1471750	RCHY1	cis	parietal	SCAN
rs1471750	C4orf22	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79275400-79310600	Weak transcription	Aorta	Aorta
2	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
3	chr4:79288000-79318400	Weak transcription	Pancreas	Pancrea
4	chr4:79290200-79310800	Weak transcription	Brain Anterior Caudate	brain
5	chr4:79291200-79308400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:79291200-79314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:79291800-79306400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:79291800-79307200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:79291800-79318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:79292000-79312000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr4:79292200-79306600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:79292200-79308400	Weak transcription	Fetal Lung	lung
13	chr4:79292200-79312200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:79292400-79310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:79292400-79312000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:79295400-79301800	Weak transcription	Psoas Muscle	Psoas
17	chr4:79295600-79338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:79297600-79301800	Weak transcription	Fetal Kidney	kidney
19	chr4:79297600-79310800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:79298000-79308000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:79299400-79302000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:79299400-79308600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:79300200-79302000	Enhancers	NHEK	skin
24	chr4:79300200-79302400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:79300200-79302400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:79300200-79302400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:79300400-79301800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:79300400-79302200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:79300400-79302400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:79300400-79302400	Enhancers	HMEC	breast
31	chr4:79300400-79303000	Strong transcription	HepG2	liver
32	chr4:79300600-79302200	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr4:79300800-79301800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:79300800-79302000	Enhancers	Fetal Intestine Small	intestine
35	chr4:79300800-79302400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:79300800-79302400	Enhancers	Fetal Heart	heart
37	chr4:79300800-79313200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:79301000-79302200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:79301000-79302400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:79301200-79302000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:79301200-79302000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr4:79301200-79302000	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr4:79301200-79302000	Enhancers	A549	lung
44	chr4:79301200-79302400	Enhancers	Fetal Intestine Large	intestine
45	chr4:79301200-79302400	Enhancers	HSMMtube	muscle
46	chr4:79301200-79305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:79301400-79302200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr4:79301600-79302000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr4:79301600-79302000	Enhancers	NH-A	brain
50	chr4:79301600-79302200	Enhancers	Duodenum Mucosa	Duodenum

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