Variant report

Variant	rs12514650
Chromosome Location	chr5:179060382-179060383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179054324..179056626-chr5:179057842..179060388,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11249650	0.88[ASN][1000 genomes]
rs11249651	0.84[ASN][1000 genomes]
rs11740867	0.84[ASN][1000 genomes]
rs12188476	0.88[ASN][1000 genomes]
rs12517588	0.90[ASN][1000 genomes]
rs12518041	0.88[ASN][1000 genomes]
rs12519803	0.88[ASN][1000 genomes]
rs12519906	0.84[ASN][1000 genomes]
rs17355294	0.88[ASN][1000 genomes]
rs28533619	0.95[ASN][1000 genomes]
rs28564876	0.82[ASN][1000 genomes]
rs4128628	0.88[ASN][1000 genomes]
rs4128629	0.88[ASN][1000 genomes]
rs4535419	0.88[ASN][1000 genomes]
rs55821473	0.88[ASN][1000 genomes]
rs55837909	0.94[ASN][1000 genomes]
rs56370020	0.80[ASN][1000 genomes]
rs58788190	0.88[ASN][1000 genomes]
rs60104959	0.88[ASN][1000 genomes]
rs61408162	0.88[ASN][1000 genomes]
rs62392796	1.00[ASN][1000 genomes]
rs6891180	0.82[ASN][1000 genomes]
rs72824554	0.88[ASN][1000 genomes]
rs7442819	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv883273	chr5:179045142-179086833	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
6	nsv1033352	chr5:179056475-179086482	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1021275	chr5:179056475-179104588	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12514650	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179051600-179060600	Weak transcription	Ovary	ovary
2	chr5:179051800-179060600	Weak transcription	Fetal Kidney	kidney
3	chr5:179052000-179061400	Weak transcription	Spleen	Spleen
4	chr5:179052200-179060400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:179052200-179060400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:179052200-179060600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:179052200-179060600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:179052200-179060600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:179052200-179060600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:179052200-179060600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:179052200-179060600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:179052200-179060600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:179052200-179060600	Weak transcription	Adipose Nuclei	Adipose
14	chr5:179052200-179060600	Weak transcription	Brain Anterior Caudate	brain
15	chr5:179052200-179060600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:179052200-179060600	Weak transcription	Brain Germinal Matrix	brain
17	chr5:179052200-179060600	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:179052200-179060600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:179052200-179060600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:179052200-179060600	Weak transcription	Esophagus	oesophagus
21	chr5:179052200-179060600	Weak transcription	Fetal Brain Female	brain
22	chr5:179052200-179060600	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:179052200-179060600	Weak transcription	Gastric	stomach
24	chr5:179052200-179060600	Weak transcription	Left Ventricle	heart
25	chr5:179052200-179060600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:179052200-179060600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:179052200-179060600	Weak transcription	Right Ventricle	heart
28	chr5:179052200-179060600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr5:179052200-179060600	Weak transcription	HMEC	breast
30	chr5:179052200-179060600	Weak transcription	HSMM	muscle
31	chr5:179052200-179060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:179052200-179060800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:179052200-179085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:179052400-179060600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:179052400-179060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:179052400-179060600	Weak transcription	Fetal Heart	heart
37	chr5:179052400-179060600	Weak transcription	Fetal Lung	lung
38	chr5:179052400-179060600	Weak transcription	K562	blood
39	chr5:179052400-179060600	Weak transcription	NHLF	lung
40	chr5:179052400-179061000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:179053000-179060400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:179054600-179060600	Weak transcription	HepG2	liver
43	chr5:179054600-179061000	Weak transcription	A549	lung
44	chr5:179055200-179060600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:179056000-179060600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:179057600-179060400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:179057800-179060600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:179058800-179060600	Enhancers	Pancreas	Pancrea
49	chr5:179059400-179060600	Active TSS	Placenta	Placenta
50	chr5:179059400-179060600	Enhancers	Dnd41	blood

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