Variant report

Variant	rs71353222
Chromosome Location	chr18:12707109-12707110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12705369..12707624-chr18:12718826..12720361,2	K562	blood:
2	chr18:12699736..12702348-chr18:12705277..12708356,3	K562	blood:
3	chr18:12701252..12704007-chr18:12704390..12707416,3	K562	blood:
4	chr18:12376201..12378120-chr18:12705040..12707340,2	K562	blood:
5	chr18:12706059..12708008-chr18:12949881..12951466,2	K562	blood:
6	chr18:12700615..12704798-chr18:12705051..12713643,12	MCF-7	breast:
7	chr18:12705392..12707414-chr18:12988712..12991441,3	MCF-7	breast:
8	chr18:12693359..12696587-chr18:12706551..12708313,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141385	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000101639	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1105748	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	1.00[ASN][1000 genomes]
rs12954606	1.00[ASN][1000 genomes]
rs12955162	1.00[ASN][1000 genomes]
rs12955176	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	1.00[ASN][1000 genomes]
rs12958301	1.00[ASN][1000 genomes]
rs12958598	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961307	1.00[ASN][1000 genomes]
rs12961711	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	1.00[ASN][1000 genomes]
rs12964717	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	1.00[ASN][1000 genomes]
rs17525459	1.00[ASN][1000 genomes]
rs17525599	1.00[ASN][1000 genomes]
rs17615525	1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	1.00[ASN][1000 genomes]
rs17616124	1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34229934	1.00[ASN][1000 genomes]
rs34371240	1.00[ASN][1000 genomes]
rs34460164	1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34737110	1.00[ASN][1000 genomes]
rs34859829	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34933611	1.00[ASN][1000 genomes]
rs35082337	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35309605	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35643117	0.88[AMR][1000 genomes]
rs35686128	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	1.00[ASN][1000 genomes]
rs35864675	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351491	1.00[ASN][1000 genomes]
rs71351492	1.00[ASN][1000 genomes]
rs71351494	1.00[ASN][1000 genomes]
rs71351495	1.00[ASN][1000 genomes]
rs71351501	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71363149	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs71353222	SPIRE1	cis	Thyroid	GTEx
rs71353222	RP11-861E21.2	cis	Thyroid	GTEx
rs71353222	SLMO1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12703400-12709000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:12703800-12713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:12704000-12707400	Weak transcription	Lung	lung
4	chr18:12704200-12707200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr18:12704200-12707200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:12704200-12707600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr18:12704200-12707600	Weak transcription	Esophagus	oesophagus
8	chr18:12704200-12709600	Weak transcription	HSMMtube	muscle
9	chr18:12704200-12709800	Weak transcription	Right Ventricle	heart
10	chr18:12704200-12713000	Weak transcription	Aorta	Aorta
11	chr18:12704200-12713200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr18:12704200-12713200	Weak transcription	Psoas Muscle	Psoas
13	chr18:12704200-12726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr18:12704400-12707200	Weak transcription	Fetal Heart	heart
15	chr18:12704400-12707400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr18:12704400-12707400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr18:12704400-12707400	Weak transcription	Left Ventricle	heart
18	chr18:12704400-12707600	Weak transcription	Fetal Stomach	stomach
19	chr18:12704400-12710000	Weak transcription	NHLF	lung
20	chr18:12704600-12707600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:12704600-12708400	Weak transcription	Gastric	stomach
22	chr18:12704600-12713000	Weak transcription	Pancreas	Pancrea
23	chr18:12704800-12707200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr18:12704800-12707200	Weak transcription	HUVEC	blood vessel
25	chr18:12704800-12707400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr18:12704800-12707400	Weak transcription	A549	lung
27	chr18:12704800-12707600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr18:12704800-12727200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr18:12704800-12727800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr18:12705000-12707200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:12705000-12707200	Weak transcription	Colonic Mucosa	Colon
32	chr18:12705000-12707400	Weak transcription	Brain Anterior Caudate	brain
33	chr18:12705000-12707400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr18:12705000-12707400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr18:12705000-12707400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr18:12705000-12707400	Weak transcription	Brain Substantia Nigra	brain
37	chr18:12705000-12707400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr18:12705000-12707600	Weak transcription	Brain Hippocampus Middle	brain
39	chr18:12705000-12710400	Weak transcription	Small Intestine	intestine
40	chr18:12705000-12722400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr18:12705000-12725200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr18:12705000-12728600	Weak transcription	Stomach Mucosa	stomach
43	chr18:12705200-12707200	Weak transcription	Brain Angular Gyrus	brain
44	chr18:12705400-12708000	Strong transcription	HSMM	muscle
45	chr18:12705400-12714600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:12705400-12726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr18:12705400-12727200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr18:12705600-12707600	Weak transcription	Spleen	Spleen
49	chr18:12705600-12707800	Strong transcription	Primary B cells from cord blood	blood
50	chr18:12705600-12708400	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links