Variant report

Variant	rs13057504
Chromosome Location	chr22:31845149-31845150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:31836635-31847259..22:31936958-31958600	GM12878	blood:
2	chr22:31844458..31846488-chr22:31846838..31850631,3	K562	blood:
3	22:31836635-31847259..22:32529813-32538538	K562	blood:
4	chr22:31742672..31744282-chr22:31844664..31847017,2	MCF-7	breast:
5	22:31836635-31847259..22:32284948-32287956	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000240591	Chromatin interaction
ENSG00000227813	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1001599	0.82[EUR][1000 genomes]
rs2273249	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273251	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899164	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34538851	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34545960	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5749265	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749267	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5749268	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5749270	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5749283	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5749286	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5749291	0.82[AMR][1000 genomes]
rs5753597	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753601	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5753609	0.82[EUR][1000 genomes]
rs5753610	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753612	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753613	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753615	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753618	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs5753621	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753623	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs5753628	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753631	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753632	0.85[EUR][1000 genomes]
rs5753639	0.85[EUR][1000 genomes]
rs5753648	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753659	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5753661	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5753664	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5753665	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5753666	0.80[ASN][1000 genomes]
rs5753669	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5753671	0.82[AMR][1000 genomes]
rs5994394	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7285619	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7293171	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs738657	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8138596	0.81[EUR][1000 genomes]
rs8139625	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8141150	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8142121	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9606839	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9606843	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9606846	0.82[AMR][1000 genomes]
rs9606847	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9606848	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9606852	0.80[AMR][1000 genomes]
rs9609268	0.80[EUR][1000 genomes]
rs9609276	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609277	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9609286	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9609295	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9609296	0.87[AMR][1000 genomes]
rs9609297	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9609299	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9609301	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9609303	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9609304	0.82[AMR][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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13057504	SFI1	cis	Thyroid	GTEx
rs13057504	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31797200-31845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr22:31797200-31846200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr22:31797200-31846400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:31797200-31860600	Strong transcription	Fetal Stomach	stomach
7	chr22:31797400-31846800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr22:31797800-31846800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr22:31799000-31845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr22:31799200-31846600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr22:31804600-31847000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr22:31814000-31846400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr22:31814200-31846800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr22:31814400-31845600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr22:31814400-31845800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr22:31814400-31846800	Strong transcription	Fetal Intestine Large	intestine
17	chr22:31814800-31846600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr22:31815000-31846600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr22:31815000-31846800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr22:31815000-31868200	Strong transcription	Dnd41	blood
21	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr22:31815400-31846200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr22:31815400-31846600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr22:31815400-31846600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr22:31822200-31846600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr22:31822400-31859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr22:31826600-31846400	Strong transcription	Brain Germinal Matrix	brain
29	chr22:31827200-31846600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr22:31827600-31846600	Strong transcription	Osteobl	bone
31	chr22:31828800-31845600	Strong transcription	GM12878-XiMat	blood
32	chr22:31829600-31846400	Strong transcription	Brain Substantia Nigra	brain
33	chr22:31829600-31852000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr22:31829800-31846600	Strong transcription	HSMM	muscle
35	chr22:31831200-31850000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr22:31832600-31846400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr22:31832600-31867800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr22:31832800-31845400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr22:31832800-31846800	Strong transcription	Brain Anterior Caudate	brain
40	chr22:31833000-31845600	Strong transcription	Brain Hippocampus Middle	brain
41	chr22:31833000-31846600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr22:31833000-31846800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr22:31833200-31847200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr22:31833600-31846800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr22:31834000-31846000	Strong transcription	Fetal Intestine Small	intestine
46	chr22:31836200-31846800	Strong transcription	Adipose Nuclei	Adipose
47	chr22:31836200-31873600	Weak transcription	Stomach Mucosa	stomach
48	chr22:31836400-31845600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr22:31836800-31853000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr22:31837000-31846800	Strong transcription	Placenta	Placenta

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