Variant report

Variant	rs1138860
Chromosome Location	chr16:74655634-74655635
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74649316..74653490-chr16:74654574..74658436,6	MCF-7	breast:
2	chr16:74639257..74644662-chr16:74649340..74660012,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10400930	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12921903	0.86[ASN][1000 genomes]
rs12935075	0.82[ASN][1000 genomes]
rs13339156	0.86[ASN][1000 genomes]
rs28377859	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28502731	0.85[ASN][1000 genomes]
rs4243108	0.81[ASN][1000 genomes]
rs4271617	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4286131	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4287593	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4302071	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4316784	0.81[ASN][1000 genomes]
rs4344772	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4462623	0.81[ASN][1000 genomes]
rs4548905	0.85[ASN][1000 genomes]
rs4564599	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887776	0.85[ASN][1000 genomes]
rs4887777	0.85[ASN][1000 genomes]
rs4887779	0.87[ASN][1000 genomes]
rs4888257	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888258	0.85[ASN][1000 genomes]
rs4888259	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888260	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4888266	0.82[ASN][1000 genomes]
rs62053563	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6564145	0.81[ASN][1000 genomes]
rs6564146	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6564147	0.84[ASN][1000 genomes]
rs6564148	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564149	0.87[ASN][1000 genomes]
rs6564152	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6564153	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6564154	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564155	0.83[ASN][1000 genomes]
rs7184754	0.87[ASN][1000 genomes]
rs7185722	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7190631	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7191754	0.80[ASN][1000 genomes]
rs7193423	0.86[ASN][1000 genomes]
rs7193508	0.86[ASN][1000 genomes]
rs7193583	0.87[ASN][1000 genomes]
rs7193959	0.87[ASN][1000 genomes]
rs7194143	0.81[ASN][1000 genomes]
rs7194687	0.87[ASN][1000 genomes]
rs7195135	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7195499	0.81[ASN][1000 genomes]
rs7204804	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7205258	0.90[ASN][1000 genomes]
rs8047243	0.82[ASN][1000 genomes]
rs8048133	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8048596	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8050615	0.82[ASN][1000 genomes]
rs8050624	0.85[ASN][1000 genomes]
rs8052923	0.83[ASN][1000 genomes]
rs8053084	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8054836	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8055784	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8055803	0.84[ASN][1000 genomes]
rs8056718	0.86[ASN][1000 genomes]
rs8057279	0.86[ASN][1000 genomes]
rs8058034	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8058437	0.84[ASN][1000 genomes]
rs8058922	0.82[ASN][1000 genomes]
rs8062404	0.86[ASN][1000 genomes]
rs8062959	0.86[ASN][1000 genomes]
rs9921672	0.83[ASN][1000 genomes]
rs9927073	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9928181	0.85[ASN][1000 genomes]
rs9938833	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv833279	chr16:74490746-74663073	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
7	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	esv275138	chr16:74647795-74722907	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv2760414	chr16:74647795-74741615	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1138860	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs1138860	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs1138860	RFWD3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74641400-74655800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:74641400-74656000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:74641600-74656000	Weak transcription	Aorta	Aorta
4	chr16:74641600-74657000	Weak transcription	Gastric	stomach
5	chr16:74641600-74657800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:74641800-74655800	Weak transcription	NHEK	skin
7	chr16:74641800-74656200	Weak transcription	HUVEC	blood vessel
8	chr16:74641800-74656600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr16:74642000-74655800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:74642000-74656000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr16:74642000-74656000	Weak transcription	Left Ventricle	heart
12	chr16:74642000-74656800	Weak transcription	Liver	Liver
13	chr16:74642000-74657600	Weak transcription	Brain Hippocampus Middle	brain
14	chr16:74642000-74658200	Weak transcription	Right Ventricle	heart
15	chr16:74642200-74655800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr16:74642200-74656000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr16:74642200-74656000	Weak transcription	Fetal Kidney	kidney
18	chr16:74642200-74656000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr16:74642200-74656400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr16:74642200-74656400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr16:74642200-74657400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr16:74642200-74688800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr16:74642400-74656200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr16:74642400-74656600	Weak transcription	HSMMtube	muscle
25	chr16:74642600-74657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr16:74643200-74655800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr16:74643800-74657000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr16:74644600-74656600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr16:74644800-74656200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr16:74644800-74657000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:74646000-74656400	Weak transcription	NHLF	lung
32	chr16:74647000-74656600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:74647600-74657600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr16:74647800-74691800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr16:74648800-74688400	Strong transcription	Dnd41	blood
36	chr16:74648800-74692200	Strong transcription	Fetal Thymus	thymus
37	chr16:74650800-74687400	Strong transcription	Thymus	Thymus
38	chr16:74651000-74655800	Weak transcription	Fetal Lung	lung
39	chr16:74651000-74691200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr16:74651200-74656400	Weak transcription	Brain Anterior Caudate	brain
41	chr16:74651200-74657000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr16:74651400-74655800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr16:74651400-74655800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr16:74652000-74656600	Weak transcription	Colon Smooth Muscle	Colon
45	chr16:74652000-74657000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr16:74652000-74664200	Weak transcription	Fetal Heart	heart
47	chr16:74652000-74674600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr16:74652000-74686000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:74652000-74692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr16:74652200-74657000	Weak transcription	Esophagus	oesophagus

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