Variant report

Variant	rs10038122
Chromosome Location	chr5:90316643-90316644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90315172..90318619-chr5:90676163..90681010,4	MCF-7	breast:
2	chr5:90316078..90318522-chr5:90323384..90326123,2	K562	blood:
3	chr5:90312914..90314737-chr5:90316544..90319036,2	K562	blood:
4	chr5:90313237..90315031-chr5:90316021..90318044,2	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10055587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10058319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10454910	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12652491	0.84[ASN][1000 genomes]
rs12657388	0.82[ASN][1000 genomes]
rs12658697	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13152882	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1828177	0.88[CEU][hapmap]
rs1828178	0.88[CEU][hapmap]
rs1848481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1848483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848484	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858070	0.88[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1976565	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048217	0.87[CEU][hapmap]
rs2367185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662281	0.81[EUR][1000 genomes]
rs2697547	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4386756	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4391205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689544	0.88[CEU][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs951948	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs998788	0.83[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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10038122	GPR98	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90308600-90318400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:90309800-90323200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:90313200-90318200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:90313400-90318400	Weak transcription	A549	lung
5	chr5:90313400-90321600	Weak transcription	Liver	Liver
6	chr5:90313600-90321400	Weak transcription	Small Intestine	intestine
7	chr5:90313800-90320000	Weak transcription	Adipose Nuclei	Adipose
8	chr5:90314000-90319200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:90314200-90319800	Weak transcription	Fetal Stomach	stomach
10	chr5:90314200-90320800	Weak transcription	Fetal Intestine Large	intestine
11	chr5:90314400-90317400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:90314400-90318400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:90314800-90316800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:90314800-90323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:90314800-90327000	Weak transcription	Gastric	stomach
16	chr5:90315000-90317400	Weak transcription	Psoas Muscle	Psoas
17	chr5:90315000-90318400	Weak transcription	Fetal Intestine Small	intestine
18	chr5:90315200-90317400	Weak transcription	Fetal Lung	lung
19	chr5:90315200-90317400	Weak transcription	K562	blood
20	chr5:90315200-90317600	Weak transcription	Stomach Mucosa	stomach
21	chr5:90315200-90318000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:90315200-90319800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:90315400-90317000	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:90315400-90318400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:90316200-90317800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr5:90316200-90318800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:90316400-90318400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:90316600-90317000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:90316600-90317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:90316600-90318000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:90316600-90323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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