Variant report

Variant	rs6876679
Chromosome Location	chr5:179053197-179053198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179053065-179053682	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:

Variant related genes	Relation type
HNRNPH1	TF binding region
ENSG00000204659	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10066669	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10076293	0.87[ASN][1000 genomes]
rs1136267	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13162707	0.89[ASN][1000 genomes]
rs28544040	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078141	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4131080	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4376229	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv823357	chr5:179046318-179058193	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6876679	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	chr5:179052000-179054200	Weak transcription	A549	lung
4	chr5:179052000-179058200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:179052000-179061400	Weak transcription	Spleen	Spleen
6	chr5:179052200-179053200	Enhancers	HepG2	liver
7	chr5:179052200-179053600	Enhancers	Liver	Liver
8	chr5:179052200-179054200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:179052200-179055800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:179052200-179056200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:179052200-179056200	Weak transcription	Fetal Intestine Small	intestine
12	chr5:179052200-179058800	Weak transcription	Pancreas	Pancrea
13	chr5:179052200-179059000	Weak transcription	Fetal Intestine Large	intestine
14	chr5:179052200-179059200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:179052200-179059200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:179052200-179059200	Weak transcription	Fetal Stomach	stomach
17	chr5:179052200-179059400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:179052200-179059400	Weak transcription	Fetal Thymus	thymus
19	chr5:179052200-179059400	Weak transcription	Lung	lung
20	chr5:179052200-179059400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:179052200-179060200	Weak transcription	Stomach Mucosa	stomach
22	chr5:179052200-179060400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:179052200-179060400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:179052200-179060600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:179052200-179060600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:179052200-179060600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:179052200-179060600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:179052200-179060600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:179052200-179060600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:179052200-179060600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:179052200-179060600	Weak transcription	Adipose Nuclei	Adipose
32	chr5:179052200-179060600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:179052200-179060600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:179052200-179060600	Weak transcription	Brain Germinal Matrix	brain
35	chr5:179052200-179060600	Weak transcription	Brain Hippocampus Middle	brain
36	chr5:179052200-179060600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:179052200-179060600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:179052200-179060600	Weak transcription	Esophagus	oesophagus
39	chr5:179052200-179060600	Weak transcription	Fetal Brain Female	brain
40	chr5:179052200-179060600	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:179052200-179060600	Weak transcription	Gastric	stomach
42	chr5:179052200-179060600	Weak transcription	Left Ventricle	heart
43	chr5:179052200-179060600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr5:179052200-179060600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:179052200-179060600	Weak transcription	Right Ventricle	heart
46	chr5:179052200-179060600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:179052200-179060600	Weak transcription	HMEC	breast
48	chr5:179052200-179060600	Weak transcription	HSMM	muscle
49	chr5:179052200-179060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:179052200-179060800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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