Variant report

Variant	rs6886107
Chromosome Location	chr5:179052185-179052186
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179049952-179052251	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:179046855-179052674	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:179047240-179052213	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr5:179049961-179052266	ECC-1	luminal epithelium:	n/a	n/a
5	TCF7L2	chr5:179050159-179052197	HCT-116	colon:	n/a	chr5:179051922-179051936 chr5:179051966-179051976 chr5:179051969-179051976
6	POLR2A	chr5:179051960-179052194	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUN	chr5:179049464-179052256	K562	blood:	n/a	n/a
8	MXI1	chr5:179049479-179052331	IMR90	lung:	n/a	n/a
9	POLR2A	chr5:179046899-179052266	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:179049964-179052197	H1-hESC	embryonic stem cell:	n/a	n/a
11	HCFC1	chr5:179048393-179052243	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr5:179052060-179052210	BJ	skin:	n/a	n/a
13	POLR2A	chr5:179049601-179052228	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:179051109..179052652-chr5:179157575..179159893,2	K562	blood:
2	chr5:179047278..179052613-chr5:179246048..179251997,13	K562	blood:
3	chr5:178985192..178988541-chr5:179048594..179052191,5	MCF-7	breast:
4	chr5:179047637..179052326-chr5:179245599..179249536,7	K562	blood:
5	chr5:178986094..178988194-chr5:179049451..179052935,4	MCF-7	breast:
6	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
7	chr5:178975871..178983601-chr5:179047224..179052413,15	K562	blood:
8	chr12:7072083..7074369-chr5:179050327..179052683,2	MCF-7	breast:
9	chr5:178975440..178984076-chr5:179047224..179053131,17	K562	blood:
10	chr17:73178705..73180897-chr5:179050924..179052648,2	MCF-7	breast:
11	chr5:179048548..179052839-chr5:179221765..179224480,6	MCF-7	breast:
12	chr5:179049048..179052854-chr5:179122221..179127718,16	MCF-7	breast:
13	chr5:179047558..179053114-chr5:179123905..179129187,22	K562	blood:
14	chr5:179049195..179052432-chr5:179232038..179235083,3	K562	blood:
15	chr5:179048168..179052824-chr5:179156969..179161337,9	MCF-7	breast:
16	chr5:179049533..179052334-chr5:179104256..179107492,4	MCF-7	breast:
17	chr5:179045239..179052804-chr5:179123707..179130726,40	K562	blood:
18	chr5:178992676..178996882-chr5:179050015..179052234,4	K562	blood:

No data

Variant related genes	Relation type
HNRNPH1	TF binding region
ENSG00000204659	Chromatin interaction
ENSG00000271969	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000207713	Chromatin interaction
ENSG00000126749	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000257084	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000207708	Chromatin interaction
ENSG00000188612	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs4331859	0.85[CHB][hapmap]
rs4364351	0.85[CHB][hapmap]
rs4700813	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs4700817	0.82[ASN][1000 genomes]
rs4701135	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs4701144	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs72824544	0.82[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6886107	RAB24	cis	parietal	SCAN
rs6886107	TRIM7	cis	cerebellum	SCAN
rs6886107	CLTB	cis	parietal	SCAN
rs6886107	C14orf142	trans	multi-tissue	Pritchard
rs6886107	LTC4S	cis	cerebellum	SCAN
rs6886107	BTNL3	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179051000-179052200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:179051000-179052200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:179051000-179052200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179051000-179052200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr5:179051000-179052200	Flanking Active TSS	HSMM	muscle
6	chr5:179051200-179052200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:179051200-179052200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr5:179051200-179052200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr5:179051200-179052200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr5:179051200-179052200	Flanking Active TSS	Dnd41	blood
11	chr5:179051200-179052200	Flanking Active TSS	K562	blood
12	chr5:179051400-179052200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:179051400-179052200	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr5:179051400-179052200	Flanking Active TSS	Fetal Brain Female	brain
15	chr5:179051400-179052200	Flanking Active TSS	Fetal Lung	lung
16	chr5:179051400-179052200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr5:179051400-179052200	Flanking Active TSS	Hela-S3	cervix
18	chr5:179051600-179052200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:179051600-179052200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:179051600-179052200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:179051600-179052200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:179051600-179052200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:179051600-179052200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr5:179051600-179052200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:179051600-179052200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:179051600-179052200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:179051600-179052200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:179051600-179052200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:179051600-179052200	Flanking Active TSS	Liver	Liver
30	chr5:179051600-179052200	Enhancers	Lung	lung
31	chr5:179051600-179052200	Enhancers	Small Intestine	intestine
32	chr5:179051600-179052200	Flanking Active TSS	HepG2	liver
33	chr5:179051600-179052200	Flanking Active TSS	NHDF-Ad	bronchial
34	chr5:179051600-179052400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:179051600-179052400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr5:179051600-179052400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:179051600-179060600	Weak transcription	Ovary	ovary
38	chr5:179051800-179052200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:179051800-179052200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:179051800-179052200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr5:179051800-179052200	Enhancers	Primary B cells from peripheral blood	blood
42	chr5:179051800-179052200	Enhancers	Primary T cells from cord blood	blood
43	chr5:179051800-179052200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr5:179051800-179052200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:179051800-179052200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr5:179051800-179052200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr5:179051800-179052200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:179051800-179052200	Enhancers	Brain Cingulate Gyrus	brain
49	chr5:179051800-179052200	Enhancers	Brain Substantia Nigra	brain
50	chr5:179051800-179052200	Enhancers	Colonic Mucosa	Colon

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