Variant report

Variant	rs871775
Chromosome Location	chr5:95158768-95158769
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	BHLHE40	chr5:95157735-95158918	GM12878	blood:	n/a	n/a
2	TCF7L2	chr5:95157814-95158787	Hela-S3	cervix:	n/a	n/a
3	WRNIP1	chr5:95157037-95159481	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:95158050-95158871	SK-N-MC	brain:	n/a	n/a
5	ZKSCAN1	chr5:95158250-95158865	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr5:95157827-95158777	K562	blood:	n/a	n/a
7	POLR2A	chr5:95156822-95160771	GM12891	blood:	n/a	n/a
8	TEAD4	chr5:95158265-95158936	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr5:95156897-95160393	GM12892	blood:	n/a	n/a
10	TAF1	chr5:95158050-95158799	Hela-S3	cervix:	n/a	n/a
11	CHD1	chr5:95156831-95160568	IMR90	lung:	n/a	n/a
12	CUX1	chr5:95158079-95158886	K562	blood:	n/a	n/a
13	TBP	chr5:95157691-95160265	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:95157670-95160015	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:95158174-95158850	HCT-116	colon:	n/a	n/a
16	JUND	chr5:95157811-95159082	K562	blood:	n/a	chr5:95158033-95158042
17	POLR2A	chr5:95157243-95160260	GM15510	blood:	n/a	n/a
18	TCF7L2	chr5:95157761-95158776	HCT-116	colon:	n/a	n/a
19	BACH1	chr5:95158536-95158853	H1-hESC	embryonic stem cell:	n/a	n/a
20	CEBPB	chr5:95158427-95158778	IMR90	lung:	n/a	n/a
21	FOS	chr5:95158425-95158855	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr5:95157774-95160184	IMR90	lung:	n/a	n/a
23	POLR2A	chr5:95158039-95158806	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUN	chr5:95158421-95158786	K562	blood:	n/a	n/a
25	POLR2A	chr5:95156816-95160353	GM18505	blood:	n/a	n/a
26	RCOR1	chr5:95156804-95160777	IMR90	lung:	n/a	n/a
27	TEAD4	chr5:95158190-95158821	HepG2	liver:	n/a	n/a
28	USF2	chr5:95158205-95158775	Hela-S3	cervix:	n/a	n/a
29	MYC	chr5:95158344-95158815	MCF10A-Er-Src	breast:	n/a	n/a
30	RELA	chr5:95157583-95159280	GM10847	blood:	n/a	n/a
31	STAT3	chr5:95158340-95158825	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr5:95157646-95160475	U87	brain:	n/a	n/a
33	CHD2	chr5:95157790-95160287	GM12878	blood:	n/a	n/a
34	RELA	chr5:95157699-95160289	GM15510	blood:	n/a	n/a
35	RELA	chr5:95157182-95158854	GM19099	blood:	n/a	n/a
36	CTCF	chr5:95158720-95158870	AG10803	skin:	n/a	n/a
37	POLR2A	chr5:95156795-95160390	GM19099	blood:	n/a	n/a
38	MAX	chr5:95157692-95158790	NB4	blood:	n/a	n/a
39	SMARCC1	chr5:95158214-95160757	Hela-S3	cervix:	n/a	n/a
40	MAFK	chr5:95158417-95158863	K562	blood:	n/a	chr5:95158697-95158711 chr5:95158699-95158710
41	IRF1	chr5:95157769-95159010	K562	blood:	n/a	chr5:95158844-95158858 chr5:95158144-95158158 chr5:95158838-95158848 chr5:95158836-95158856 chr5:95158842-95158856 chr5:95158841-95158855 chr5:95158843-95158860 chr5:95158842-95158855 chr5:95158844-95158855 chr5:95158842-95158855 chr5:95158840-95158854 chr5:95158844-95158854 chr5:95158838-95158852
42	POLR2A	chr5:95156904-95160434	GM12878	blood:	n/a	n/a
43	MAZ	chr5:95157878-95158825	Hela-S3	cervix:	n/a	n/a
44	JUND	chr5:95158369-95158962	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr5:95157739-95158956	PBDE	blood:	n/a	n/a
46	MXI1	chr5:95158240-95159463	GM12878	blood:	n/a	n/a
47	STAT3	chr5:95158340-95158841	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr5:95158469-95158920	Hela-S3	cervix:	n/a	chr5:95158844-95158855
49	JUND	chr5:95158275-95158990	HCT-116	colon:	n/a	n/a
50	POLR2A	chr5:95156951-95158805	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:94890265..94891768-chr5:95158248..95160600,2	K562	blood:
2	chr5:95157133..95161008-chr5:95170364..95173601,6	MCF-7	breast:
3	chr16:31191124..31191940-chr5:95158038..95158783,2	Hela-S3	cervix:

Variant related genes	Relation type
GLRX	TF binding region
ENSG00000164291	Chromatin interaction
ENSG00000251000	Chromatin interaction
ENSG00000198677	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11135439	1.00[YRI][hapmap]
rs11750758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2546197	0.93[GIH][hapmap];0.84[YRI][hapmap]
rs29000870	0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs60014999	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7726424	0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv462255	chr5:95142817-95168155	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv598961	chr5:95142817-95168155	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs871775	C5orf27	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95153200-95160400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr5:95154800-95159000	Active TSS	NHLF	lung
3	chr5:95155000-95159200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:95156400-95158800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:95156600-95158800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:95156600-95158800	Active TSS	GM12878-XiMat	blood
7	chr5:95156800-95158800	Active TSS	HSMMtube	muscle
8	chr5:95156800-95159800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr5:95157000-95158800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr5:95157000-95158800	Active TSS	Brain Cingulate Gyrus	brain
11	chr5:95157200-95158800	Active TSS	Primary T cells fromperipheralblood	blood
12	chr5:95157200-95158800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:95157200-95158800	Active TSS	Aorta	Aorta
14	chr5:95157200-95158800	Active TSS	Thymus	Thymus
15	chr5:95157200-95159000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:95157200-95159000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr5:95157200-95159000	Active TSS	Right Ventricle	heart
18	chr5:95157200-95159400	Active TSS	Psoas Muscle	Psoas
19	chr5:95157200-95159800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:95157200-95160000	Active TSS	Brain Anterior Caudate	brain
21	chr5:95157400-95158800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:95157400-95158800	Active TSS	Ovary	ovary
23	chr5:95157400-95158800	Active TSS	HSMM	muscle
24	chr5:95157600-95158800	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr5:95157600-95158800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr5:95157600-95158800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:95157600-95158800	Active TSS	Brain Germinal Matrix	brain
28	chr5:95157600-95158800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr5:95157600-95158800	Active TSS	Left Ventricle	heart
30	chr5:95157600-95158800	Active TSS	Monocytes-CD14+_RO01746	blood
31	chr5:95157600-95158800	Active TSS	NHDF-Ad	bronchial
32	chr5:95157600-95159000	Active TSS	Lung	lung
33	chr5:95157600-95159000	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr5:95157600-95159600	Active TSS	Colonic Mucosa	Colon
35	chr5:95157600-95159600	Active TSS	Right Atrium	heart
36	chr5:95157600-95160400	Flanking Active TSS	K562	blood
37	chr5:95157800-95158800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:95157800-95158800	Active TSS	Osteobl	bone
39	chr5:95158000-95158800	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr5:95158000-95159000	Active TSS	Fetal Muscle Trunk	muscle
41	chr5:95158200-95158800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:95158200-95158800	Flanking Active TSS	NHEK	skin
43	chr5:95158200-95160000	Flanking Active TSS	HUVEC	blood vessel
44	chr5:95158200-95160200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:95158200-95160200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:95158200-95160400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr5:95158400-95158800	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr5:95158400-95158800	Flanking Active TSS	Fetal Stomach	stomach
49	chr5:95158400-95158800	Active TSS	HepG2	liver
50	chr5:95158400-95159000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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