Variant report

Variant	rs7718673
Chromosome Location	chr5:178980009-178980010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:178976811..178980871-chr5:179039605..179043375,3	K562	blood:
2	chr5:178977892..178980462-chr5:179104901..179106460,2	MCF-7	breast:
3	chr5:178979685..178981544-chr5:178981841..178984975,3	K562	blood:
4	chr5:178975440..178984076-chr5:179047224..179053131,17	K562	blood:
5	chr5:178979685..178981490-chr5:178983248..178984975,2	K562	blood:
6	chr5:178979256..178982161-chr5:178989561..178991785,2	K562	blood:
7	chr5:178975871..178983601-chr5:179047224..179052413,15	K562	blood:
8	chr5:178978852..178982589-chr5:179047122..179052388,6	MCF-7	breast:
9	chr5:178976329..178981059-chr5:179123787..179127407,6	K562	blood:
10	chr5:178976021..178979527-chr5:178979544..178984972,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225051	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10064596	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10069256	0.80[ASN][1000 genomes]
rs10072757	0.80[CHD][hapmap]
rs10074573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10078712	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078796	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479541	0.80[ASN][1000 genomes]
rs10479542	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12652495	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12658664	0.80[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13179470	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13183521	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2411380	0.80[ASN][1000 genomes]
rs34102807	0.80[ASN][1000 genomes]
rs4700835	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4700836	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4701130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[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]
rs4701131	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]
rs4701132	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6869842	0.80[ASN][1000 genomes]
rs6889447	0.84[CEU][hapmap];0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs6895321	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6896112	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6896940	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7380974	0.80[ASN][1000 genomes]
rs7702303	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7703730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7704349	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7723230	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733389	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7736163	0.92[AMR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7718673	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs7718673	RUFY1	cis	cerebellum	SCAN
rs7718673	C5orf45	cis	cerebellum	SCAN
rs7718673	HNRNPH1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178977000-178980200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:178978600-178980200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:178978600-178980400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:178978600-178980400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr5:178978600-178980400	Enhancers	Fetal Brain Male	brain
6	chr5:178978600-178981000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:178978600-178981000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr5:178978600-178981200	Enhancers	Left Ventricle	heart
9	chr5:178978600-178981400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:178978600-178981600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:178978600-178986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:178978800-178980400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr5:178978800-178980600	Enhancers	Primary B cells from cord blood	blood
14	chr5:178978800-178980800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:178978800-178980800	Weak transcription	HSMMtube	muscle
16	chr5:178978800-178981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:178978800-178981000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr5:178978800-178981000	Enhancers	Adipose Nuclei	Adipose
19	chr5:178978800-178981200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:178978800-178981800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr5:178978800-178985600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:178978800-178985600	Weak transcription	Fetal Brain Female	brain
23	chr5:178978800-178986000	Weak transcription	Aorta	Aorta
24	chr5:178978800-178986200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:178979000-178980200	Enhancers	Liver	Liver
26	chr5:178979000-178980400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr5:178979000-178980400	Genic enhancers	Fetal Thymus	thymus
28	chr5:178979000-178980600	Enhancers	Psoas Muscle	Psoas
29	chr5:178979000-178980800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:178979000-178981000	Enhancers	Brain Cingulate Gyrus	brain
31	chr5:178979000-178981000	Enhancers	HMEC	breast
32	chr5:178979000-178981200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:178979000-178981200	Enhancers	Thymus	Thymus
34	chr5:178979000-178981400	Enhancers	Esophagus	oesophagus
35	chr5:178979000-178981600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:178979000-178981600	Enhancers	NH-A	brain
37	chr5:178979000-178985600	Weak transcription	HSMM	muscle
38	chr5:178979200-178980200	Enhancers	Fetal Lung	lung
39	chr5:178979200-178980200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr5:178979200-178980400	Enhancers	Placenta	Placenta
41	chr5:178979200-178980400	Enhancers	Small Intestine	intestine
42	chr5:178979200-178980600	Genic enhancers	Fetal Muscle Leg	muscle
43	chr5:178979200-178981200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr5:178979200-178981200	Enhancers	Brain Angular Gyrus	brain
45	chr5:178979200-178981200	Genic enhancers	Fetal Intestine Small	intestine
46	chr5:178979200-178981400	Enhancers	Spleen	Spleen
47	chr5:178979200-178981600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:178979200-178981600	Enhancers	HUVEC	blood vessel
49	chr5:178979400-178980200	Enhancers	Primary hematopoietic stem cells	blood
50	chr5:178979400-178980200	Enhancers	Stomach Mucosa	stomach

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