Variant report

Variant	rs17721193
Chromosome Location	chr1:247457854-247457855
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:247457619-247458034	IMR90	lung:	n/a	n/a
2	FOS	chr1:247457779-247457860	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:247457733-247457872	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:247457604-247457970	U87	brain:	n/a	n/a
5	RCOR1	chr1:247457532-247458237	IMR90	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:247457841-247457891	AoSMC	blood vessel:	n/a
2	chr1:247457841-247457891	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:247457841-247457891	HEK293	kidney:	embryo
4	chr1:247457841-247457891	AG09319	gingival:	n/a
5	chr1:247457841-247457891	HCF	heart:	n/a
6	chr1:247457841-247457891	BE2_C	brain:	n/a
7	chr1:247457841-247457891	SKMC	muscle:	n/a
8	chr1:247457841-247457891	HAEpiC	amniotic membrane:	n/a
9	chr1:247457841-247457891	NT2-D1	testis:	n/a
10	chr1:247457841-247457891	U87	brain:	n/a
11	chr1:247457841-247457891	Jurkat	blood:	n/a
12	chr1:247457841-247457891	GM19239	blood:	n/a
13	chr1:247457841-247457891	GM12891	blood:	n/a
14	chr1:247457841-247457891	HCT-116	colon:	n/a
15	chr1:247457841-247457891	AG04450	lung:	fetal
16	chr1:247457841-247457891	PrEC	prostate:	n/a
17	chr1:247457841-247457891	HL-60	blood:	n/a
18	chr1:247457841-247457891	ovcar-3	ovarian:	n/a
19	chr1:247457841-247457891	HRE	kidney:	n/a
20	chr1:247457841-247457891	AG10803	skin:	n/a
21	chr1:247457841-247457891	AG04449	skin:	fetal
22	chr1:247457841-247457891	HRCEpiC	kidney:	n/a
23	chr1:247457841-247457891	NB4	blood:	n/a
24	chr1:247457841-247457891	SK-N-SH_RA	brain:	n/a
25	chr1:247457841-247457891	A549	lung:	n/a
26	chr1:247457841-247457891	GM12878	blood:	n/a
27	chr1:247457841-247457891	HepG2	liver:	n/a
28	chr1:247457841-247457891	ProgFib	skin:	n/a
29	chr1:247457841-247457891	NHBE	bronchial:	n/a
30	chr1:247457841-247457891	PANC-1	pancreas:	n/a
31	chr1:247457841-247457891	IMR90	lung:	fetal
32	chr1:247457841-247457891	BJ	skin:	n/a
33	chr1:247457841-247457891	HCM	heart:	n/a
34	chr1:247457841-247457891	HUVEC	blood vessel:	n/a
35	chr1:247457841-247457891	NHDF-neo	bronchial:	n/a
36	chr1:247457841-247457891	GM12892	blood:	n/a
37	chr1:247457841-247457891	MCF10A-Er-Src	breast:	n/a
38	chr1:247457841-247457891	HEEpiC	esophagus:	n/a
39	chr1:247457841-247457891	SK-N-MC	brain:	n/a
40	chr1:247457841-247457891	NH-A	brain:	n/a
41	chr1:247457841-247457891	HMEC	breast:	n/a
42	chr1:247457841-247457891	ECC-1	luminal epithelium:	n/a
43	chr1:247457841-247457891	HIPEpiC	eye:	n/a
44	chr1:247457841-247457891	GM06990	blood:	n/a
45	chr1:247457841-247457891	CMK	blood:	n/a
46	chr1:247457841-247457891	RPTEC	kidney:	n/a
47	chr1:247457841-247457891	HNPCEpiC	eye:	n/a
48	chr1:247457841-247457891	SAEC	small airway:	n/a
49	chr1:247457841-247457891	AG09309	skin:	n/a
50	chr1:247457841-247457891	SK-N-SH	brain:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247455319..247457914-chr1:247494277..247496616,2	MCF-7	breast:
2	chr1:247456054..247458907-chr1:247476595..247478143,2	K562	blood:
3	chr1:247456296..247458047-chr1:247490288..247491803,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202079	TF binding region
ENSG00000202079	CpG island
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10754543	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10802482	0.86[EUR][1000 genomes]
rs10802483	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11579352	0.88[ASN][1000 genomes]
rs11581163	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12081945	0.85[EUR][1000 genomes]
rs12082983	0.90[EUR][1000 genomes]
rs12564303	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566166	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771918	0.86[EUR][1000 genomes]
rs1778552	0.86[EUR][1000 genomes]
rs1778553	0.85[EUR][1000 genomes]
rs2211273	0.91[EUR][1000 genomes]
rs2890342	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41268345	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4925606	0.90[EUR][1000 genomes]
rs4925620	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55686936	0.90[EUR][1000 genomes]
rs55913685	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56124448	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56245379	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56250713	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56358050	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57647632	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57653401	1.00[ASN][1000 genomes]
rs58747962	0.94[ASN][1000 genomes]
rs61838684	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838689	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61841570	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426236	0.91[EUR][1000 genomes]
rs6426238	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6656258	0.90[EUR][1000 genomes]
rs6667658	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6698384	0.91[EUR][1000 genomes]
rs6698803	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7544023	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552041	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17721193	EXO1	cis	parietal	SCAN
rs17721193	VN1R5	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:247451600-247460400	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
11	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:247453200-247460400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:247453400-247462000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
16	chr1:247454400-247461800	Enhancers	Fetal Thymus	thymus
17	chr1:247454600-247458000	Enhancers	K562	blood
18	chr1:247454800-247458400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:247454800-247458400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:247454800-247459800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:247455000-247458400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:247455000-247460000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
24	chr1:247455200-247460000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:247455200-247460200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:247455200-247461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:247455400-247459800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:247455400-247461200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:247455600-247459000	Enhancers	NH-A	brain
31	chr1:247455600-247462600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:247455800-247459000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:247455800-247459800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:247455800-247460800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:247455800-247462200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:247455800-247462600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:247456000-247462000	Weak transcription	Lung	lung
39	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
40	chr1:247456200-247459200	Enhancers	Osteobl	bone
41	chr1:247456200-247460800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:247456200-247462200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:247456600-247458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
45	chr1:247456800-247462000	Weak transcription	Ovary	ovary
46	chr1:247456800-247462200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr1:247456800-247462400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:247457000-247458000	Enhancers	HSMMtube	muscle
49	chr1:247457000-247459800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:247457000-247460400	Weak transcription	Fetal Stomach	stomach

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