Variant report

Variant	rs28630797
Chromosome Location	chr4:649876-649877
allele	C/T
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	MAZ	chr4:649743-649943	HepG2	liver:	n/a	chr4:649898-649905
2	POLR2A	chr4:649826-649920	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr4:649783-649934	K562	blood:	n/a	n/a
4	MAX	chr4:648843-650038	HepG2	liver:	n/a	chr4:649898-649905
5	BHLHE40	chr4:649384-649973	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:649845-649895	NT2-D1	testis:	n/a
2	chr4:649845-649895	HL-60	blood:	n/a
3	chr4:649845-649895	SK-N-SH_RA	brain:	n/a
4	chr4:649845-649895	LNCaP	prostate:	n/a
5	chr4:649845-649895	IMR90	lung:	fetal
6	chr4:649845-649895	HIPEpiC	eye:	n/a
7	chr4:649845-649895	NH-A	brain:	n/a
8	chr4:649845-649895	HNPCEpiC	eye:	n/a
9	chr4:649845-649895	HCPEpiC	choroid plexus:	n/a
10	chr4:649845-649895	Jurkat	blood:	n/a
11	chr4:649845-649895	NB4	blood:	n/a
12	chr4:649845-649895	ECC-1	luminal epithelium:	n/a
13	chr4:649845-649895	MCF-7	breast:	n/a
14	chr4:649845-649895	MCF10A-Er-Src	breast:	n/a
15	chr4:649845-649895	Hepatocyte	liver:	n/a
16	chr4:649845-649895	HPAEpiC	pulmonary alveolar:	n/a
17	chr4:649845-649895	K562	blood:	n/a
18	chr4:649845-649895	GM06990	blood:	n/a
19	chr4:649845-649895	HCM	heart:	n/a
20	chr4:649845-649895	PANC-1	pancreas:	n/a
21	chr4:649845-649895	HCF	heart:	n/a
22	chr4:649845-649895	HRPEpiC	eye:	n/a
23	chr4:649845-649895	RPTEC	kidney:	n/a
24	chr4:649845-649895	HRE	kidney:	n/a
25	chr4:649845-649895	A549	lung:	n/a
26	chr4:649845-649895	ovcar-3	ovarian:	n/a
27	chr4:649845-649895	HAEpiC	amniotic membrane:	n/a
28	chr4:649845-649895	U87	brain:	n/a
29	chr4:649845-649895	AoSMC	blood vessel:	n/a
30	chr4:649845-649895	AG04450	lung:	fetal
31	chr4:649845-649895	HEK293	kidney:	embryo
32	chr4:649845-649895	BJ	skin:	n/a
33	chr4:649845-649895	AG09319	gingival:	n/a
34	chr4:649845-649895	HRCEpiC	kidney:	n/a
35	chr4:649845-649895	AG09309	skin:	n/a
36	chr4:649845-649895	BE2_C	brain:	n/a
37	chr4:649845-649895	ProgFib	skin:	n/a
38	chr4:649845-649895	SKMC	muscle:	n/a
39	chr4:649845-649895	AG04449	skin:	fetal
40	chr4:649845-649895	AG10803	skin:	n/a
41	chr4:649845-649895	NHBE	bronchial:	n/a
42	chr4:649845-649895	GM19239	blood:	n/a
43	chr4:649845-649895	T-47D	breast:	n/a
44	chr4:649845-649895	HMEC	breast:	n/a
45	chr4:649845-649895	H1-hESC	embryonic stem cell:	embryo
46	chr4:649845-649895	Hela-S3	cervix:	n/a
47	chr4:649845-649895	GM12891	blood:	n/a
48	chr4:649845-649895	PrEC	prostate:	n/a
49	chr4:649845-649895	GM12878	blood:	n/a
50	chr4:649845-649895	Caco-2	colon:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr4:644808..646339-chr4:648173..650037,2	K562	blood:
2	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:
3	chr4:642131..644821-chr4:649750..652284,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242686	TF binding region
ENSG00000242686	CpG island
ENSG00000242686	Chromatin interaction
ENSG00000133256	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10027549	1.00[ASN][1000 genomes]
rs10027866	0.90[AFR][1000 genomes]
rs10030136	1.00[ASN][1000 genomes]
rs10031745	0.85[AFR][1000 genomes]
rs1135375	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119162	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28374488	0.90[AFR][1000 genomes]
rs28470912	1.00[ASN][1000 genomes]
rs28483373	1.00[ASN][1000 genomes]
rs28488910	1.00[ASN][1000 genomes]
rs28520978	0.90[AFR][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	1.00[ASN][1000 genomes]
rs28583078	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28586910	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28588872	0.91[AFR][1000 genomes]
rs28600205	0.91[AFR][1000 genomes]
rs28742266	1.00[ASN][1000 genomes]
rs28742899	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864130	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864131	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3891250	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934459	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4463020	1.00[ASN][1000 genomes]
rs4505760	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4518182	1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71602496	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056602	1.00[ASN][1000 genomes]
rs73058406	1.00[ASN][1000 genomes]
rs7436737	1.00[ASN][1000 genomes]
rs9991613	1.00[ASN][1000 genomes]
rs9992641	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking 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 miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv10412	chr4:649291-651178	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28630797	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs28630797	RP11-1191J2.2	cis	Thyroid	GTEx
rs28630797	RP11-1191J2.2	cis	lung	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:645800-656800	Weak transcription	Gastric	stomach
8	chr4:646800-650600	Enhancers	Brain Angular Gyrus	brain
9	chr4:647000-650000	Enhancers	Brain Anterior Caudate	brain
10	chr4:647200-651200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr4:648400-650200	Enhancers	Brain Substantia Nigra	brain
12	chr4:648400-657000	Weak transcription	Right Ventricle	heart
13	chr4:648600-650000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr4:648600-650600	Enhancers	Spleen	Spleen
15	chr4:648800-650000	Flanking Bivalent TSS/Enh	HepG2	liver
16	chr4:648800-650800	Enhancers	Brain Cingulate Gyrus	brain
17	chr4:648800-653400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:649000-651000	Enhancers	Brain Hippocampus Middle	brain
19	chr4:649000-652800	Weak transcription	Brain Germinal Matrix	brain
20	chr4:649200-652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:649200-653000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:649400-650000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:649600-650000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:649600-650000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:649800-651000	Weak transcription	Pancreas	Pancrea
26	chr4:649800-653200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:649800-655600	Weak transcription	Thymus	Thymus

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