Variant report

Variant	rs1398337
Chromosome Location	chr5:9548098-9548099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:9547640-9548135	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr5:9547703-9548141	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:9547205-9548187	ProgFib	skin:	n/a	n/a
4	TEAD4	chr5:9547716-9548188	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:9547693-9548102	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:9544189-9548175	IMR90	lung:	n/a	n/a
7	YY1	chr5:9547754-9548115	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr5:9547311-9548203	IMR90	lung:	n/a	chr5:9547846-9547860
9	TBP	chr5:9547685-9548171	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr5:9544024-9548426	IMR90	lung:	n/a	chr5:9547821-9547831 chr5:9545804-9545814 chr5:9547149-9547159 chr5:9545538-9545548

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:9548098-9548148	SAEC	small airway:	n/a
2	chr5:9548098-9548148	HMEC	breast:	n/a
3	chr5:9548098-9548148	RPTEC	kidney:	n/a
4	chr5:9548098-9548148	HL-60	blood:	n/a
5	chr5:9548098-9548148	AG04449	skin:	fetal
6	chr5:9548098-9548148	SK-N-SH	brain:	n/a
7	chr5:9548098-9548148	HPAEpiC	pulmonary alveolar:	n/a
8	chr5:9548098-9548148	A549	lung:	n/a
9	chr5:9548098-9548148	HUVEC	blood vessel:	n/a
10	chr5:9548098-9548148	GM19239	blood:	n/a
11	chr5:9548098-9548148	HNPCEpiC	eye:	n/a
12	chr5:9548098-9548148	HIPEpiC	eye:	n/a
13	chr5:9548098-9548148	HRPEpiC	eye:	n/a
14	chr5:9548098-9548148	Hepatocyte	liver:	n/a
15	chr5:9548098-9548148	Caco-2	colon:	n/a
16	chr5:9548098-9548148	NT2-D1	testis:	n/a
17	chr5:9548098-9548148	Jurkat	blood:	n/a
18	chr5:9548098-9548148	MCF-7	breast:	n/a
19	chr5:9548098-9548148	PrEC	prostate:	n/a
20	chr5:9548098-9548148	HepG2	liver:	n/a
21	chr5:9548098-9548148	ovcar-3	ovarian:	n/a
22	chr5:9548098-9548148	T-47D	breast:	n/a
23	chr5:9548098-9548148	U87	brain:	n/a
24	chr5:9548098-9548148	HRE	kidney:	n/a
25	chr5:9548098-9548148	NHBE	bronchial:	n/a
26	chr5:9548098-9548148	AG09319	gingival:	n/a
27	chr5:9548098-9548148	CMK	blood:	n/a
28	chr5:9548098-9548148	AG04450	lung:	fetal
29	chr5:9548098-9548148	IMR90	lung:	fetal
30	chr5:9548098-9548148	NB4	blood:	n/a
31	chr5:9548098-9548148	HEEpiC	esophagus:	n/a
32	chr5:9548098-9548148	NH-A	brain:	n/a
33	chr5:9548098-9548148	HCM	heart:	n/a
34	chr5:9548098-9548148	SK-N-SH_RA	brain:	n/a
35	chr5:9548098-9548148	GM12892	blood:	n/a
36	chr5:9548098-9548148	Hela-S3	cervix:	n/a
37	chr5:9548098-9548148	AoSMC	blood vessel:	n/a
38	chr5:9548098-9548148	HRCEpiC	kidney:	n/a
39	chr5:9548098-9548148	HEK293	kidney:	embryo
40	chr5:9548098-9548148	SK-N-MC	brain:	n/a
41	chr5:9548098-9548148	HCF	heart:	n/a
42	chr5:9548098-9548148	K562	blood:	n/a
43	chr5:9548098-9548148	GM06990	blood:	n/a
44	chr5:9548098-9548148	GM12891	blood:	n/a
45	chr5:9548098-9548148	PFSK-1	brain:	n/a
46	chr5:9548098-9548148	BE2_C	brain:	n/a
47	chr5:9548098-9548148	MCF10A-Er-Src	breast:	n/a
48	chr5:9548098-9548148	HAEpiC	amniotic membrane:	n/a
49	chr5:9548098-9548148	BJ	skin:	n/a
50	chr5:9548098-9548148	AG09309	skin:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr5:9546514..9548478-chr5:9550572..9552547,2	K562	blood:
2	chr5:9546585..9548880-chr5:9563821..9566752,2	K562	blood:
3	chr5:9546664..9548240-chr5:9561037..9563217,2	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA5A	TF binding region
SNORD123	TF binding region
SNORD123	CpG island
SEMA5A	CpG island

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10462868	0.98[ASN][1000 genomes]
rs11749803	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1508798	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1614229	0.88[CHB][hapmap];0.84[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1651283	0.80[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1651284	1.00[JPT][hapmap]
rs1651285	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1651286	0.98[ASN][1000 genomes]
rs1706987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706992	0.94[ASN][1000 genomes]
rs17263917	0.89[CEU][hapmap]
rs268555	0.90[ASN][1000 genomes]
rs268556	0.90[ASN][1000 genomes]
rs374218	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798099	0.90[ASN][1000 genomes]
rs414396	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414829	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs422309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs431288	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs456885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs460234	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs461337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs461750	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs464621	0.90[ASN][1000 genomes]
rs56344213	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60322708	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs605126	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73051829	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv597073	chr5:9533854-9550642	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1398337	CTD-2001E22.2	cis	lung	GTEx
rs1398337	CTD-2001E22.2	cis	Adipose Subcutaneous	GTEx
rs1398337	CTD-2001E22.2	cis	Artery Aorta	GTEx
rs1398337	CTD-2001E22.2	cis	Muscle Skeletal	GTEx
rs1398337	FASTKD3	cis	parietal	SCAN
rs1398337	CTD-2001E22.2	cis	Esophagus Mucosa	GTEx
rs1398337	CTD-2001E22.2	cis	Nerve Tibial	GTEx
rs1398337	CTD-2001E22.2	cis	Heart Left Ventricle	GTEx
rs1398337	DAP	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9542800-9548400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:9543000-9548200	Active TSS	Aorta	Aorta
3	chr5:9543200-9548200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:9543200-9548200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:9543200-9548200	Active TSS	Right Atrium	heart
6	chr5:9543400-9548400	Active TSS	NHLF	lung
7	chr5:9543600-9548400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr5:9543800-9548200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:9543800-9548200	Active TSS	Fetal Kidney	kidney
10	chr5:9543800-9548600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:9543800-9548800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:9543800-9548800	Active TSS	Placenta Amnion	Placenta Amnion
13	chr5:9544200-9548400	Active TSS	NHDF-Ad	bronchial
14	chr5:9544400-9548200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr5:9544400-9548400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:9544400-9548400	Active TSS	Osteobl	bone
17	chr5:9544600-9548400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:9544600-9548600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr5:9545200-9548400	Active TSS	Duodenum Mucosa	Duodenum
20	chr5:9545400-9548200	Active TSS	Brain Germinal Matrix	brain
21	chr5:9545600-9548600	Active TSS	HMEC	breast
22	chr5:9545800-9548200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:9546000-9548400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:9546000-9548400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:9546600-9548200	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr5:9546800-9548200	Active TSS	Colonic Mucosa	Colon
27	chr5:9547000-9548200	Enhancers	Liver	Liver
28	chr5:9547000-9554200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:9547200-9548200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr5:9547200-9548200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:9547200-9548200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr5:9547200-9548200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:9547200-9548200	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr5:9547200-9548200	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr5:9547200-9548200	Flanking Active TSS	Fetal Stomach	stomach
36	chr5:9547200-9548200	Flanking Active TSS	Left Ventricle	heart
37	chr5:9547200-9548200	Flanking Active TSS	NHEK	skin
38	chr5:9547400-9548200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:9547400-9548200	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr5:9547400-9548200	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr5:9547400-9548200	Enhancers	HUVEC	blood vessel
42	chr5:9547600-9548200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:9547600-9548200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr5:9547600-9548200	Active TSS	Stomach Mucosa	stomach
45	chr5:9547600-9548400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:9547600-9548400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr5:9547800-9548200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr5:9547800-9548200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:9547800-9548200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:9547800-9548200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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