Variant report

Variant	rs60913149
Chromosome Location	chr12:56643684-56643685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56632067..56634668-chr12:56642933..56645753,2	K562	blood:
2	chr12:56632924..56644144-chr12:56648283..56654213,19	MCF-7	breast:
3	chr12:56635398..56637749-chr12:56642367..56644284,3	MCF-7	breast:
4	chr12:56636502..56647526-chr12:56648654..56655042,17	K562	blood:
5	chr12:56628855..56631009-chr12:56641714..56643835,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139540	Chromatin interaction
ENSG00000139645	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11171803	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171806	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575224	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575229	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575234	0.82[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274490	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274493	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274496	0.82[EUR][1000 genomes]
rs1295772	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118431	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118439	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes]
rs2020854	0.87[ASN][1000 genomes]
rs2066807	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066808	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066818	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2066819	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291361	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306693	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306694	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371494	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2629447	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2629452	0.88[EUR][1000 genomes]
rs2643623	0.84[ASN][1000 genomes]
rs2643626	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695782	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695788	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695789	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35526714	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41392645	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41423244	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57367440	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59822547	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59917308	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60542959	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs744051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773652	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773664	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773665	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs808919	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs60913149	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs60913149	RP11-977G19.11	cis	Artery Aorta	GTEx
rs60913149	RP11-977G19.11	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56624400-56646000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:56628600-56644600	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:56628600-56649800	Strong transcription	Fetal Stomach	stomach
4	chr12:56629000-56649400	Strong transcription	Thymus	Thymus
5	chr12:56629000-56650400	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:56629200-56649600	Strong transcription	Brain Germinal Matrix	brain
7	chr12:56629200-56650000	Strong transcription	Liver	Liver
8	chr12:56629200-56650200	Strong transcription	Brain Anterior Caudate	brain
9	chr12:56629400-56649600	Strong transcription	Fetal Muscle Leg	muscle
10	chr12:56629600-56649600	Strong transcription	Fetal Brain Female	brain
11	chr12:56629800-56649400	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:56629800-56649800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr12:56629800-56650000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:56629800-56650200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56629800-56650200	Strong transcription	Primary T cells from cord blood	blood
16	chr12:56630000-56644600	Strong transcription	Lung	lung
17	chr12:56630000-56648600	Strong transcription	Dnd41	blood
18	chr12:56630000-56649400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:56630000-56649600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:56630000-56649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:56630000-56649800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:56630000-56650200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:56630000-56650600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:56630200-56650000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:56630400-56644400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:56630400-56650200	Strong transcription	Fetal Thymus	thymus
27	chr12:56630600-56650400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:56631000-56650000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:56631800-56649400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:56632200-56650200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr12:56632400-56650200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:56632600-56650200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:56632600-56650200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:56632800-56649600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:56632800-56649600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:56632800-56650000	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr12:56632800-56650000	Strong transcription	NHEK	skin
38	chr12:56633000-56650000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:56633000-56650200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:56633000-56650200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:56633000-56650400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:56633000-56650600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr12:56633200-56649600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:56633200-56650000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:56633200-56650600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:56633400-56649600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr12:56633400-56649800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:56633400-56650000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:56633400-56650000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:56633600-56650600	Strong transcription	Primary monocytes fromperipheralblood	blood

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