Variant report

Variant	rs6564159
Chromosome Location	chr16:74713054-74713055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:74712874-74713096	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr16:74712887-74713066	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74700450..74705009-chr16:74710570..74714672,7	MCF-7	breast:
2	chr16:74708894..74711247-chr16:74711417..74714110,3	K562	blood:

Variant related genes	Relation type
MLKL	TF binding region
ENSG00000168404	Chromatin interaction
ENSG00000262904	Chromatin interaction
ENSG00000168411	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12445991	0.85[JPT][hapmap]
rs12448026	0.85[JPT][hapmap]
rs12932878	0.86[ASN][1000 genomes]
rs28639983	0.93[AFR][1000 genomes]
rs35505591	0.86[ASN][1000 genomes]
rs4072222	0.85[JPT][hapmap]
rs4438331	0.85[JPT][hapmap]
rs4887776	0.85[JPT][hapmap]
rs4887777	0.85[JPT][hapmap]
rs4887779	0.85[JPT][hapmap]
rs4887784	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888266	0.85[JPT][hapmap]
rs4888275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6564154	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs6564157	0.81[JPT][hapmap]
rs6564158	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7193959	0.85[JPT][hapmap]
rs7194143	0.85[JPT][hapmap]
rs7196369	0.85[JPT][hapmap]
rs7204382	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs7204804	0.85[JPT][hapmap]
rs7205258	0.85[JPT][hapmap]
rs7342732	0.85[JPT][hapmap]
rs8050624	0.85[JPT][hapmap]
rs8052923	0.85[JPT][hapmap]
rs8055784	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs8058692	0.85[JPT][hapmap]
rs8058922	0.80[CEU][hapmap]
rs9927073	0.85[JPT][hapmap]
rs9929483	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs9931225	0.85[JPT][hapmap]
rs9932831	0.85[JPT][hapmap]
rs9938833	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	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
5	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
6	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	67 gene(s)	inside rSNPs	diseases
7	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
8	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
10	nsv906907	chr16:74702254-74785902	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6564159	FA2H	cis	cerebellum	SCAN
rs6564159	MLKL	cis	lymphoblastoid	seeQTL
rs6564159	MLKL	cis	multi-tissue	Pritchard
rs6564159	RFWD3	cis	multi-tissue	Pritchard

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74701600-74730000	Weak transcription	Stomach Mucosa	stomach
2	chr16:74701800-74715400	Weak transcription	Brain Angular Gyrus	brain
3	chr16:74701800-74724600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr16:74701800-74725400	Weak transcription	Ovary	ovary
5	chr16:74701800-74725400	Weak transcription	NHLF	lung
6	chr16:74701800-74729600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:74701800-74729800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr16:74701800-74730000	Weak transcription	Brain Substantia Nigra	brain
9	chr16:74701800-74734000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:74702000-74713400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr16:74702000-74713600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:74702000-74725000	Weak transcription	Fetal Intestine Large	intestine
13	chr16:74702000-74725200	Weak transcription	Fetal Muscle Leg	muscle
14	chr16:74702000-74725200	Weak transcription	NHDF-Ad	bronchial
15	chr16:74702000-74725400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr16:74702000-74729600	Weak transcription	Brain Anterior Caudate	brain
17	chr16:74702000-74730000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:74705000-74725000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr16:74705200-74713600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr16:74705200-74717200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr16:74705200-74718000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr16:74705400-74713400	Strong transcription	Hela-S3	cervix
23	chr16:74705400-74714400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr16:74705400-74714800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr16:74705400-74717000	Strong transcription	Primary T cells from cord blood	blood
26	chr16:74705400-74718200	Strong transcription	Lung	lung
27	chr16:74705400-74719600	Strong transcription	Liver	Liver
28	chr16:74705400-74719800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:74705400-74719800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr16:74705400-74720000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr16:74705400-74723000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr16:74705400-74727200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr16:74705400-74728600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr16:74705400-74729200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr16:74705400-74729200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr16:74705400-74729600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr16:74705400-74729600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr16:74705600-74713600	Strong transcription	Adipose Nuclei	Adipose
39	chr16:74705600-74714600	Strong transcription	Thymus	Thymus
40	chr16:74705600-74720000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr16:74705600-74720200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr16:74705800-74720800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr16:74705800-74723000	Strong transcription	Spleen	Spleen
44	chr16:74705800-74723800	Weak transcription	HMEC	breast
45	chr16:74706400-74730000	Weak transcription	NH-A	brain
46	chr16:74706600-74718000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr16:74707000-74729600	Weak transcription	Colon Smooth Muscle	Colon
48	chr16:74707200-74714200	Strong transcription	Fetal Intestine Small	intestine
49	chr16:74707200-74714400	Strong transcription	Esophagus	oesophagus
50	chr16:74707600-74713400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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