Variant report

Variant	rs6879412
Chromosome Location	chr5:179108977-179108978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179104126..179107921-chr5:179108631..179111977,3	K562	blood:
2	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
3	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
4	chr5:179108514..179110108-chr5:179117962..179119813,2	K562	blood:
5	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:
6	chr5:179105005..179107336-chr5:179108581..179112647,5	MCF-7	breast:

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

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11249655	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249656	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249657	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249658	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11749559	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11750523	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188238	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12515399	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518476	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28674071	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28846185	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55702506	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56159807	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60216315	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406697	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406698	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67484565	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7379093	0.80[ASN][1000 genomes]
rs7719302	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9637934	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9637935	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9763971	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6879412	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179106400-179118200	Weak transcription	Right Ventricle	heart
2	chr5:179106600-179109400	Weak transcription	Left Ventricle	heart
3	chr5:179106600-179109800	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:179106600-179109800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:179106600-179110000	Weak transcription	Fetal Stomach	stomach
6	chr5:179106600-179112600	Weak transcription	Brain Anterior Caudate	brain
7	chr5:179106600-179113600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:179106600-179124200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:179106600-179124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:179106800-179109800	Weak transcription	Lung	lung
11	chr5:179106800-179110200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:179106800-179110600	Weak transcription	Thymus	Thymus
13	chr5:179106800-179123000	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:179107400-179109600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:179107400-179121400	Weak transcription	Primary B cells from cord blood	blood
16	chr5:179107600-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:179107600-179111000	Weak transcription	Stomach Mucosa	stomach
18	chr5:179107600-179117600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:179107600-179119600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:179107600-179123200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:179107600-179123200	Weak transcription	Fetal Thymus	thymus
22	chr5:179107600-179123400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:179107800-179114400	Weak transcription	Spleen	Spleen
24	chr5:179108000-179109000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:179108000-179110800	Weak transcription	GM12878-XiMat	blood
26	chr5:179108000-179115600	Weak transcription	Brain Substantia Nigra	brain
27	chr5:179108200-179110800	Weak transcription	Pancreas	Pancrea
28	chr5:179108400-179109200	Enhancers	HepG2	liver
29	chr5:179108400-179109800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr5:179108400-179123000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:179108600-179109800	Weak transcription	Esophagus	oesophagus
32	chr5:179108600-179112400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:179108600-179123600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:179108800-179109800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:179108800-179111000	Weak transcription	Liver	Liver

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