Variant report

Variant	rs12935075
Chromosome Location	chr16:74676033-74676034
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74674399..74676570-chr16:74676599..74678795,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168411	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10400930	0.87[ASN][1000 genomes]
rs1138860	0.82[ASN][1000 genomes]
rs12921903	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13339156	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28377859	0.88[ASN][1000 genomes]
rs28502731	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4072222	0.87[ASN][1000 genomes]
rs4072450	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4243108	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4271617	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4286131	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4287593	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4302071	0.87[ASN][1000 genomes]
rs4316784	0.80[ASN][1000 genomes]
rs4344772	0.85[ASN][1000 genomes]
rs4462623	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4544266	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4548905	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4564599	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4588013	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4887776	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887777	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887779	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4888257	0.80[ASN][1000 genomes]
rs4888258	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4888259	0.86[ASN][1000 genomes]
rs4888266	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888270	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57488599	0.87[ASN][1000 genomes]
rs58136167	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6564145	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6564146	0.85[ASN][1000 genomes]
rs6564147	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564148	0.86[ASN][1000 genomes]
rs6564149	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6564152	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6564153	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6564154	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564155	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6564157	0.83[ASN][1000 genomes]
rs7184754	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7185722	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7190631	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7193423	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7193508	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7193583	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7193959	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7194143	0.80[ASN][1000 genomes]
rs7194687	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7195135	0.86[ASN][1000 genomes]
rs7195499	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7196627	0.86[EUR][1000 genomes]
rs7204382	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7204804	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7205258	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7342732	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8047243	0.86[ASN][1000 genomes]
rs8047523	0.87[EUR][1000 genomes]
rs8048596	0.83[ASN][1000 genomes]
rs8049056	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8050615	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8050624	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052923	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8053084	0.85[ASN][1000 genomes]
rs8055784	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8055803	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8056718	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8057279	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8058034	0.87[ASN][1000 genomes]
rs8058437	0.86[ASN][1000 genomes]
rs8058922	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8062404	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8062959	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9921672	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9925807	0.87[ASN][1000 genomes]
rs9927073	0.86[ASN][1000 genomes]
rs9928181	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9929483	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9931225	0.85[ASN][1000 genomes]
rs9938833	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12935075	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx
rs12935075	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs12935075	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs12935075	RFWD3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74642200-74688800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:74647800-74691800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr16:74648800-74688400	Strong transcription	Dnd41	blood
4	chr16:74648800-74692200	Strong transcription	Fetal Thymus	thymus
5	chr16:74650800-74687400	Strong transcription	Thymus	Thymus
6	chr16:74651000-74691200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr16:74652000-74686000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:74652000-74692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr16:74652200-74685600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:74652200-74687400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr16:74652200-74699000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:74653000-74686800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr16:74653000-74687800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:74653200-74683000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr16:74653200-74685600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:74653200-74687200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr16:74653200-74687800	Strong transcription	Fetal Stomach	stomach
18	chr16:74653200-74690600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr16:74653200-74698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:74653400-74699000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:74653600-74677800	Weak transcription	Psoas Muscle	Psoas
22	chr16:74654000-74685800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr16:74654400-74689000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr16:74654600-74686000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr16:74654600-74687800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr16:74655200-74688600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr16:74655400-74686000	Strong transcription	Placenta	Placenta
28	chr16:74656800-74699400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr16:74657000-74699200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr16:74657200-74699400	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr16:74657200-74699600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr16:74657400-74684600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr16:74657400-74699200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr16:74657400-74699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr16:74657600-74685800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr16:74658200-74697200	Weak transcription	Fetal Brain Male	brain
37	chr16:74662600-74686400	Strong transcription	Adipose Nuclei	Adipose
38	chr16:74665600-74678200	Weak transcription	Small Intestine	intestine
39	chr16:74665800-74681400	Weak transcription	Right Ventricle	heart
40	chr16:74665800-74688200	Weak transcription	Stomach Mucosa	stomach
41	chr16:74666000-74692000	Weak transcription	Fetal Heart	heart
42	chr16:74666600-74677000	Weak transcription	HSMMtube	muscle
43	chr16:74666600-74677800	Weak transcription	Aorta	Aorta
44	chr16:74666600-74677800	Weak transcription	Colon Smooth Muscle	Colon
45	chr16:74666800-74676600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr16:74667800-74677200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr16:74667800-74677800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:74667800-74677800	Weak transcription	Gastric	stomach
49	chr16:74667800-74678000	Weak transcription	Esophagus	oesophagus
50	chr16:74667800-74678200	Weak transcription	Rectal Smooth Muscle	rectum

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