Variant report

Variant	rs4701131
Chromosome Location	chr5:178982446-178982447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:178979510-178983668	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:178975440..178984076-chr5:179047224..179053131,17	K562	blood:
2	chr5:178980836..178983768-chr5:179095589..179098241,2	MCF-7	breast:
3	chr5:178975871..178983601-chr5:179047224..179052413,15	K562	blood:
4	chr5:178979685..178981544-chr5:178981841..178984975,3	K562	blood:
5	chr5:178978852..178982589-chr5:179047122..179052388,6	MCF-7	breast:
6	chr5:178981570..178984338-chr5:178984530..178988621,4	K562	blood:
7	chr5:178981782..178983559-chr5:178998257..179000519,2	K562	blood:
8	chr5:178976021..178979527-chr5:178979544..178984972,9	K562	blood:

No data

Variant related genes	Relation type
RUFY1	TF binding region
ENSG00000249140	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000176783	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10064596	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10069256	0.80[ASN][1000 genomes]
rs10072757	0.80[CHD][hapmap]
rs10074573	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10078712	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078796	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479541	0.80[ASN][1000 genomes]
rs10479542	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12652495	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12658664	0.86[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12719865	0.80[YRI][hapmap]
rs13179470	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13183521	0.88[ASN][1000 genomes]
rs2411380	0.80[ASN][1000 genomes]
rs34102807	0.80[ASN][1000 genomes]
rs4700835	0.90[ASN][1000 genomes]
rs4700836	0.90[ASN][1000 genomes]
rs4701130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701132	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6869842	0.80[ASN][1000 genomes]
rs6889447	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs6895321	0.83[ASN][1000 genomes]
rs6896112	0.90[ASN][1000 genomes]
rs6896940	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7380974	0.80[ASN][1000 genomes]
rs7702303	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7703730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7704349	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7718673	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723230	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733389	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[ASN][1000 genomes]
rs7736163	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9286047	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
6	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
7	nsv1022509	chr5:178950829-179002751	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883269	chr5:178951106-179031595	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
10	nsv1015477	chr5:178954409-179016804	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv883271	chr5:178955046-179031595	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv883272	chr5:178961872-179031595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv1028236	chr5:178962087-179019981	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4701131	RUFY1	cis	cerebellum	SCAN
rs4701131	RUFY1	cis	multi-tissue	Pritchard
rs4701131	RUFY1	cis	parietal	SCAN
rs4701131	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs4701131	HNRPH1	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178978600-178986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:178978800-178985600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:178978800-178985600	Weak transcription	Fetal Brain Female	brain
4	chr5:178978800-178986000	Weak transcription	Aorta	Aorta
5	chr5:178978800-178986200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:178979000-178985600	Weak transcription	HSMM	muscle
7	chr5:178979400-178985600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:178979600-178984800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:178979600-178984800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:178979600-178985600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:178979600-178985600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:178979600-178985800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:178979600-178986000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:178979800-178986000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:178980000-178985600	Weak transcription	Primary T cells from cord blood	blood
16	chr5:178980000-178985800	Weak transcription	Brain Anterior Caudate	brain
17	chr5:178980000-178985800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:178980200-178983800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:178980200-178985000	Weak transcription	Liver	Liver
20	chr5:178980200-178985600	Weak transcription	Fetal Lung	lung
21	chr5:178980200-178985600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:178980200-178985800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:178980400-178982600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr5:178980400-178984600	Weak transcription	GM12878-XiMat	blood
25	chr5:178980400-178985400	Weak transcription	Fetal Brain Male	brain
26	chr5:178980400-178985600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:178980400-178985600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:178980400-178985600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:178980400-178985600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr5:178980400-178985600	Weak transcription	A549	lung
31	chr5:178980400-178985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:178980400-178985800	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:178980400-178985800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:178980400-178985800	Weak transcription	Right Atrium	heart
35	chr5:178980400-178985800	Weak transcription	NHLF	lung
36	chr5:178980400-178986000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:178980400-178986000	Weak transcription	Colonic Mucosa	Colon
38	chr5:178980400-178986000	Weak transcription	Placenta	Placenta
39	chr5:178980400-178986200	Weak transcription	Gastric	stomach
40	chr5:178980600-178985600	Weak transcription	Primary B cells from cord blood	blood
41	chr5:178980600-178986000	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:178981000-178985400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:178981000-178985600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr5:178981000-178985600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:178981000-178985800	Weak transcription	Adipose Nuclei	Adipose
46	chr5:178981000-178985800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:178981000-178985800	Weak transcription	HSMMtube	muscle
48	chr5:178981000-178986000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:178981000-178986000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:178981200-178984800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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