Variant report

Variant	rs6601048
Chromosome Location	chr5:178971837-178971838
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	chr5:178966233..178969209-chr5:178970782..178972509,2	MCF-7	breast:
2	chr5:178971437..178973246-chr5:178974311..178976700,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RUFY1-3	chr5:178971224-178972983	NONHSAT105589

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10036611	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10041685	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069256	0.84[ASN][1000 genomes]
rs10079553	0.94[ASN][1000 genomes]
rs10464056	1.00[ASN][1000 genomes]
rs10479541	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11749010	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12520676	0.85[ASN][1000 genomes]
rs12654319	0.89[ASN][1000 genomes]
rs12658811	0.83[AMR][1000 genomes]
rs13185115	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2411380	0.84[ASN][1000 genomes]
rs2411386	0.97[ASN][1000 genomes]
rs34102807	0.84[ASN][1000 genomes]
rs4701192	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601043	0.84[ASN][1000 genomes]
rs6601045	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601047	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6869842	0.84[ASN][1000 genomes]
rs6879664	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6879665	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6889447	0.84[ASN][1000 genomes]
rs6894988	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7380706	0.84[ASN][1000 genomes]
rs7380974	0.84[ASN][1000 genomes]
rs7727647	0.81[ASN][1000 genomes]
rs9286047	0.84[ASN][1000 genomes]
rs9329080	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9885443	0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6601048	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178958000-178976800	Weak transcription	Fetal Intestine Small	intestine
2	chr5:178958000-178977000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:178963600-178976400	Weak transcription	Osteobl	bone
4	chr5:178969400-178975000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:178970400-178973800	Enhancers	Primary B cells from peripheral blood	blood
6	chr5:178970400-178975200	Weak transcription	Hela-S3	cervix
7	chr5:178970600-178974000	Enhancers	Primary B cells from cord blood	blood
8	chr5:178971400-178972000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:178971400-178972000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:178971400-178972000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr5:178971400-178972400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr5:178971400-178972400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr5:178971600-178972000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:178971600-178972000	Enhancers	Fetal Thymus	thymus
15	chr5:178971800-178972000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr5:178971800-178972000	Flanking Active TSS	GM12878-XiMat	blood
17	chr5:178971800-178972200	Enhancers	Primary hematopoietic stem cells	blood
18	chr5:178971800-178976200	Weak transcription	Dnd41	blood

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