Variant report

Variant	rs12325017
Chromosome Location	chr16:74500888-74500889
allele	C/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	RUNX3	chr16:74500677-74501151	GM12878	blood:	n/a	n/a
2	CREB1	chr16:74500669-74501271	GM12878	blood:	n/a	n/a
3	RUNX3	chr16:74500700-74501151	GM12878	blood:	n/a	n/a
4	BCLAF1	chr16:74500738-74501138	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74499520..74501485-chr16:74501761..74503824,2	MCF-7	breast:
2	chr16:74489287..74491803-chr16:74498510..74501318,2	K562	blood:

Variant related genes	Relation type
GLG1	TF binding region
ENSG00000207525	TF binding region
ENSG00000251794	Chromatin interaction
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1019572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1019573	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10500587	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11149722	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1132843	0.84[ASN][1000 genomes]
rs11639812	0.94[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11640021	0.86[ASN][1000 genomes]
rs11640632	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11641958	0.81[ASN][1000 genomes]
rs11643293	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11644298	0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11647149	0.84[ASN][1000 genomes]
rs11648868	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12445991	0.92[JPT][hapmap]
rs12446054	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[ASN][1000 genomes]
rs12446095	0.85[ASN][1000 genomes]
rs12447531	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12448026	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs12449071	0.85[ASN][1000 genomes]
rs12449125	0.94[ASN][1000 genomes]
rs12598701	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13339161	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs13359	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs1469140	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17672539	0.86[ASN][1000 genomes]
rs1985611	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2098754	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs2288053	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[YRI][hapmap];0.88[ASN][1000 genomes]
rs2303275	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2303277	0.91[ASN][1000 genomes]
rs2303278	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303281	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28762730	0.82[ASN][1000 genomes]
rs35209570	0.87[ASN][1000 genomes]
rs3785312	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826239	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851729	0.92[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap]
rs3851730	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072450	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4243108	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4438331	0.92[JPT][hapmap]
rs4600490	0.82[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs4887772	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs4887776	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap]
rs4887777	0.92[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4887779	0.80[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap]
rs4888238	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4888240	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4888242	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888253	0.80[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4888256	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs4888262	0.92[JPT][hapmap]
rs4888265	0.85[JPT][hapmap]
rs4888266	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs4888267	0.90[JPT][hapmap]
rs6564117	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6564154	0.92[JPT][hapmap]
rs7185026	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7189123	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs7190577	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7191665	0.92[JPT][hapmap]
rs7193959	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7194143	0.92[JPT][hapmap]
rs7195196	0.86[ASN][1000 genomes]
rs7195198	0.86[ASN][1000 genomes]
rs7201320	0.86[JPT][hapmap]
rs7203452	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs7204804	0.92[JPT][hapmap]
rs7205258	0.82[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap]
rs7342732	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7978	0.92[JPT][hapmap];0.90[YRI][hapmap]
rs8045848	0.89[CHD][hapmap];0.84[JPT][hapmap]
rs8050624	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs8052923	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs8053599	0.87[ASN][1000 genomes]
rs8055784	0.92[JPT][hapmap]
rs8058133	0.92[JPT][hapmap]
rs8058692	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs8058922	0.84[JPT][hapmap]
rs8059869	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs8062783	0.86[JPT][hapmap]
rs918782	0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9888976	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9923145	0.92[JPT][hapmap]
rs9923616	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9927073	0.92[JPT][hapmap]
rs9931225	0.92[JPT][hapmap]
rs9932831	0.92[JPT][hapmap]
rs9938833	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1066212	chr16:74068470-74527133	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv542954	chr16:74068470-74527133	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1065964	chr16:74088091-74575604	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	34 gene(s)	inside rSNPs	diseases
5	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
6	esv2758431	chr16:74334780-74587185	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	esv2758656	chr16:74334780-74587185	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	esv2762054	chr16:74337036-74507056	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv428806	chr16:74394226-74580125	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv833278	chr16:74415944-74584123	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	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
12	nsv960357	chr16:74480805-74507776	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12325017	RFWD3	cis	multi-tissue	Pritchard
rs12325017	MLKL	cis	multi-tissue	Pritchard
rs12325017	TXNL4B	cis	cerebellum	SCAN
rs12325017	EXOSC6	cis	parietal	SCAN
rs12325017	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	chr16:74480400-74501000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr16:74480400-74501400	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr16:74480400-74502600	Strong transcription	Thymus	Thymus
4	chr16:74480400-74530800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr16:74480400-74530800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr16:74480400-74531800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:74480600-74503000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr16:74480600-74530600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:74480800-74530600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr16:74480800-74530800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:74481200-74520000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr16:74481200-74520200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr16:74481800-74519800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr16:74482000-74514600	Strong transcription	Fetal Thymus	thymus
15	chr16:74483000-74530600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr16:74483000-74530800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr16:74483200-74520000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr16:74483200-74520400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr16:74483800-74514400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr16:74483800-74530600	Strong transcription	Liver	Liver
21	chr16:74484000-74503000	Weak transcription	Stomach Mucosa	stomach
22	chr16:74484000-74513600	Strong transcription	Fetal Muscle Leg	muscle
23	chr16:74484200-74512200	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr16:74484200-74516800	Strong transcription	Fetal Stomach	stomach
25	chr16:74484400-74512400	Strong transcription	Placenta	Placenta
26	chr16:74484400-74532200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr16:74484600-74503000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:74485000-74530800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr16:74485200-74514800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr16:74485400-74512600	Strong transcription	Adipose Nuclei	Adipose
31	chr16:74485600-74542600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr16:74485800-74506000	Strong transcription	Lung	lung
33	chr16:74485800-74511400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr16:74488600-74510600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr16:74488600-74510800	Strong transcription	Ovary	ovary
36	chr16:74488600-74512600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr16:74488600-74519800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr16:74488600-74520200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr16:74488800-74510800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr16:74488800-74512200	Strong transcription	Brain Anterior Caudate	brain
41	chr16:74488800-74512400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr16:74488800-74530600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr16:74489000-74508800	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr16:74489000-74511600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr16:74489000-74520200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:74489200-74531000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr16:74489600-74510200	Strong transcription	Fetal Intestine Small	intestine
48	chr16:74489800-74506200	Strong transcription	HSMMtube	muscle
49	chr16:74490200-74503000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr16:74490400-74503200	Strong transcription	Fetal Intestine Large	intestine

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