Variant report

Variant	rs9931225
Chromosome Location	chr16:74699293-74699294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:74698291-74699444	GM12892	blood:	n/a	n/a
2	POLR2A	chr16:74697007-74699353	K562	blood:	n/a	n/a
3	POLR2A	chr16:74697046-74699481	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:74698468-74699314	K562	blood:	n/a	n/a
5	POLR2A	chr16:74698445-74699398	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr16:74698417-74699714	GM12878	blood:	n/a	n/a
7	POLR2A	chr16:74699010-74699297	K562	blood:	n/a	n/a
8	POLR2A	chr16:74698470-74699579	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr16:74698651-74702053	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr16:74699125-74699428	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:74698318-74699705	GM12892	blood:	n/a	n/a
12	HEY1	chr16:74697140-74700066	K562	blood:	n/a	n/a
13	POLR2A	chr16:74698171-74699322	GM12892	blood:	n/a	n/a
14	POLR2A	chr16:74697564-74700009	K562	blood:	n/a	n/a
15	POLR2A	chr16:74698675-74699312	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74640131..74642133-chr16:74699118..74701416,2	MCF-7	breast:
2	chr16:74698718..74701799-chr16:74732753..74735845,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000262904	TF binding region
ENSG00000168404	Chromatin interaction
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1019572	0.92[JPT][hapmap]
rs1019573	0.92[JPT][hapmap]
rs10400930	0.81[ASN][1000 genomes]
rs11639812	0.92[JPT][hapmap]
rs11644298	0.92[JPT][hapmap]
rs11648868	0.92[JPT][hapmap]
rs12325017	0.92[JPT][hapmap]
rs12445991	1.00[JPT][hapmap]
rs12448026	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs12598701	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs12716769	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12921903	0.83[ASN][1000 genomes]
rs12935075	0.85[ASN][1000 genomes]
rs13339156	0.83[ASN][1000 genomes]
rs13339161	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1469140	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2098754	0.92[JPT][hapmap];0.85[MKK][hapmap]
rs2303275	0.92[JPT][hapmap]
rs2303278	0.92[JPT][hapmap]
rs2303281	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs28377859	0.83[ASN][1000 genomes]
rs28502731	0.82[ASN][1000 genomes]
rs28681530	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4072222	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4072450	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4243108	0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.91[ASN][1000 genomes]
rs4271617	0.87[ASN][1000 genomes]
rs4286131	0.87[ASN][1000 genomes]
rs4287593	0.87[ASN][1000 genomes]
rs4302071	0.82[ASN][1000 genomes]
rs4438331	1.00[JPT][hapmap]
rs4462623	0.91[ASN][1000 genomes]
rs4548905	0.82[ASN][1000 genomes]
rs4564599	0.86[ASN][1000 genomes]
rs4588013	0.82[ASN][1000 genomes]
rs4600490	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4887772	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4887776	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4887777	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4887779	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4888253	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4888256	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap]
rs4888258	0.82[ASN][1000 genomes]
rs4888259	0.80[ASN][1000 genomes]
rs4888262	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4888264	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4888265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4888266	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4888267	0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4888270	0.94[ASN][1000 genomes]
rs4888271	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4888274	0.89[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56099065	0.86[AMR][1000 genomes]
rs57488599	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58136167	0.92[ASN][1000 genomes]
rs6564117	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs6564147	0.80[ASN][1000 genomes]
rs6564148	0.80[ASN][1000 genomes]
rs6564149	0.82[ASN][1000 genomes]
rs6564152	0.83[ASN][1000 genomes]
rs6564153	0.83[ASN][1000 genomes]
rs6564154	0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.87[ASN][1000 genomes]
rs6564155	0.88[ASN][1000 genomes]
rs6564157	0.92[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs6564159	0.85[JPT][hapmap]
rs7184754	0.86[ASN][1000 genomes]
rs7185026	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap]
rs7185722	0.83[ASN][1000 genomes]
rs7188880	0.89[EUR][1000 genomes]
rs7189123	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7190631	0.82[ASN][1000 genomes]
rs7191665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7193423	0.83[ASN][1000 genomes]
rs7193508	0.83[ASN][1000 genomes]
rs7193583	0.82[ASN][1000 genomes]
rs7193959	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7194143	1.00[JPT][hapmap]
rs7194687	0.82[ASN][1000 genomes]
rs7195499	0.91[ASN][1000 genomes]
rs7196369	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs7201320	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7203452	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap]
rs7204382	0.82[CHB][hapmap];0.82[CHD][hapmap];0.88[MKK][hapmap];0.85[ASN][1000 genomes]
rs7204804	0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs7205258	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7342732	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.94[ASN][1000 genomes]
rs8045848	0.92[JPT][hapmap]
rs8047243	0.80[ASN][1000 genomes]
rs8049056	0.81[ASN][1000 genomes]
rs8050624	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.88[ASN][1000 genomes]
rs8052367	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8052923	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8055784	0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.93[ASN][1000 genomes]
rs8056718	0.81[ASN][1000 genomes]
rs8057279	0.83[ASN][1000 genomes]
rs8058034	0.81[ASN][1000 genomes]
rs8058133	0.88[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8058692	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs8058922	0.83[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.88[MKK][hapmap];0.87[ASN][1000 genomes]
rs8059780	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8059869	0.85[JPT][hapmap]
rs8061942	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8062404	0.81[ASN][1000 genomes]
rs8062783	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8062959	0.83[ASN][1000 genomes]
rs918782	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap]
rs9888976	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9922988	0.82[EUR][1000 genomes]
rs9923145	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9923616	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9927073	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap]
rs9928181	0.82[ASN][1000 genomes]
rs9929483	0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9929496	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9929931	0.85[EUR][1000 genomes]
rs9932831	1.00[JPT][hapmap]
rs9938833	0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	nsv572975	chr16:74677312-74702254	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9931225	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs9931225	RFWD3	cis	Whole Blood	GTEx
rs9931225	RFWD3	cis	parietal	SCAN
rs9931225	RFWD3	cis	Esophagus Mucosa	GTEx
rs9931225	CYB5B	cis	parietal	SCAN
rs9931225	MLKL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74656800-74699400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr16:74657200-74699400	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr16:74657200-74699600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr16:74657400-74699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr16:74678600-74699800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr16:74685000-74700000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr16:74685800-74699400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
8	chr16:74687200-74699800	Weak transcription	Right Atrium	heart
9	chr16:74688000-74699400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr16:74689200-74699600	Strong transcription	Fetal Intestine Small	intestine
11	chr16:74689200-74699800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:74689800-74699600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:74690000-74699400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr16:74692000-74699400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:74692400-74699800	Weak transcription	Stomach Mucosa	stomach
16	chr16:74692600-74699400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr16:74692800-74700400	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr16:74695000-74699800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr16:74695200-74699800	Weak transcription	Fetal Kidney	kidney
20	chr16:74695400-74699800	Weak transcription	Colon Smooth Muscle	Colon
21	chr16:74695400-74699800	Weak transcription	Pancreas	Pancrea
22	chr16:74695400-74699800	Weak transcription	Psoas Muscle	Psoas
23	chr16:74695400-74700200	Weak transcription	Aorta	Aorta
24	chr16:74696200-74699400	Strong transcription	Fetal Intestine Large	intestine
25	chr16:74696200-74699600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr16:74696400-74699400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:74697200-74699400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr16:74697400-74699400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:74697800-74699400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr16:74697800-74699400	Genic enhancers	Fetal Thymus	thymus
31	chr16:74697800-74699600	Genic enhancers	K562	blood
32	chr16:74698000-74699400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr16:74698000-74699600	Weak transcription	HSMM	muscle
34	chr16:74698000-74699800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr16:74698000-74699800	Weak transcription	Brain Angular Gyrus	brain
36	chr16:74698000-74700200	Weak transcription	Small Intestine	intestine
37	chr16:74698200-74699400	Weak transcription	Fetal Brain Male	brain
38	chr16:74698200-74699600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr16:74698200-74699800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr16:74698200-74699800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr16:74698200-74699800	Weak transcription	Brain Hippocampus Middle	brain
42	chr16:74698200-74699800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr16:74698200-74699800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr16:74698200-74699800	Weak transcription	HSMMtube	muscle
45	chr16:74698200-74700000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr16:74698400-74699400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr16:74698400-74699400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
48	chr16:74698400-74699800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr16:74698400-74699800	Weak transcription	Colonic Mucosa	Colon
50	chr16:74698400-74699800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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