Variant report

Variant	rs1938300
Chromosome Location	chr1:45672783-45672784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr1:45671804-45672826	MCF-7	breast:	n/a	chr1:45672052-45672062 chr1:45672049-45672059 chr1:45672103-45672112 chr1:45672130-45672139 chr1:45672239-45672248
2	REST	chr1:45670473-45672843	H1-neurons	neurons:	n/a	n/a
3	GATA2	chr1:45672574-45672960	HUVEC	blood vessel:	n/a	n/a
4	RCOR1	chr1:45671744-45672802	Hela-S3	cervix:	n/a	n/a
5	ZKSCAN1	chr1:45671739-45673236	Hela-S3	cervix:	n/a	n/a
6	MXI1	chr1:45671342-45672807	IMR90	lung:	n/a	n/a
7	GATA3	chr1:45672570-45672926	T-47D	breast:	n/a	n/a
8	GATA3	chr1:45672587-45673296	SH-SY5Y	brain:	n/a	n/a
9	POLR2A	chr1:45671241-45672825	H1-neurons	neurons:	n/a	n/a
10	SIN3A	chr1:45670734-45672798	H1-hESC	embryonic stem cell:	n/a	n/a
11	SMC3	chr1:45672300-45673055	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:45671606-45672830	H1-neurons	neurons:	n/a	n/a
13	MXI1	chr1:45670219-45673038	SK-N-SH	brain:	n/a	n/a
14	GATA2	chr1:45672554-45672963	SH-SY5Y	brain:	n/a	n/a
15	SIN3AK20	chr1:45671228-45672793	PANC-1	pancreas:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45672735-45672785	NH-A	brain:	n/a
2	chr1:45672735-45672785	Caco-2	colon:	n/a
3	chr1:45672735-45672785	HRPEpiC	eye:	n/a
4	chr1:45672735-45672785	Jurkat	blood:	n/a
5	chr1:45672735-45672785	PANC-1	pancreas:	n/a
6	chr1:45672735-45672785	SK-N-MC	brain:	n/a
7	chr1:45672735-45672785	HIPEpiC	eye:	n/a
8	chr1:45672735-45672785	T-47D	breast:	n/a
9	chr1:45672735-45672785	LNCaP	prostate:	n/a
10	chr1:45672735-45672785	GM12878	blood:	n/a
11	chr1:45672735-45672785	AG09309	skin:	n/a
12	chr1:45672735-45672785	PrEC	prostate:	n/a
13	chr1:45672735-45672785	AG04450	lung:	fetal
14	chr1:45672735-45672785	RPTEC	kidney:	n/a
15	chr1:45672735-45672785	HUVEC	blood vessel:	n/a
16	chr1:45672735-45672785	HAEpiC	amniotic membrane:	n/a
17	chr1:45672735-45672785	BJ	skin:	n/a
18	chr1:45672735-45672785	HCF	heart:	n/a
19	chr1:45672735-45672785	BE2_C	brain:	n/a
20	chr1:45672735-45672785	GM19239	blood:	n/a
21	chr1:45672735-45672785	HepG2	liver:	n/a
22	chr1:45672735-45672785	NHBE	bronchial:	n/a
23	chr1:45672735-45672785	HCT-116	colon:	n/a
24	chr1:45672735-45672785	MCF-7	breast:	n/a
25	chr1:45672735-45672785	GM12892	blood:	n/a
26	chr1:45672735-45672785	MCF10A-Er-Src	breast:	n/a
27	chr1:45672735-45672785	ECC-1	luminal epithelium:	n/a
28	chr1:45672735-45672785	HNPCEpiC	eye:	n/a
29	chr1:45672735-45672785	PFSK-1	brain:	n/a
30	chr1:45672735-45672785	AoSMC	blood vessel:	n/a
31	chr1:45672735-45672785	HRE	kidney:	n/a
32	chr1:45672735-45672785	Hepatocyte	liver:	n/a
33	chr1:45672735-45672785	CMK	blood:	n/a
34	chr1:45672735-45672785	AG09319	gingival:	n/a
35	chr1:45672735-45672785	GM12891	blood:	n/a
36	chr1:45672735-45672785	AG10803	skin:	n/a
37	chr1:45672735-45672785	ProgFib	skin:	n/a
38	chr1:45672735-45672785	IMR90	lung:	fetal
39	chr1:45672735-45672785	SK-N-SH	brain:	n/a
40	chr1:45672735-45672785	HEEpiC	esophagus:	n/a
41	chr1:45672735-45672785	SK-N-SH_RA	brain:	n/a
42	chr1:45672735-45672785	HL-60	blood:	n/a
43	chr1:45672735-45672785	U87	brain:	n/a
44	chr1:45672735-45672785	HCM	heart:	n/a
45	chr1:45672735-45672785	HEK293	kidney:	embryo
46	chr1:45672735-45672785	Hela-S3	cervix:	n/a
47	chr1:45672735-45672785	ovcar-3	ovarian:	n/a
48	chr1:45672735-45672785	A549	lung:	n/a
49	chr1:45672735-45672785	NB4	blood:	n/a
50	chr1:45672735-45672785	SKMC	muscle:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45480075..45485962-chr1:45670647..45674355,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPDL-1	chr1:45672409-45675890	NONHSAT002922

No data

Variant related genes	Relation type
ZSWIM5	TF binding region
ZSWIM5	CpG island
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10789454	0.85[EUR][1000 genomes]
rs11211074	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1144868	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806438	0.98[ASN][1000 genomes]
rs11810239	0.97[ASN][1000 genomes]
rs1226670	0.98[ASN][1000 genomes]
rs1226733	0.97[ASN][1000 genomes]
rs1226734	0.97[ASN][1000 genomes]
rs1226735	0.82[ASN][1000 genomes]
rs1226746	0.98[ASN][1000 genomes]
rs1226747	0.98[ASN][1000 genomes]
rs1226748	0.98[ASN][1000 genomes]
rs1226836	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1226914	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1782459	0.95[ASN][1000 genomes]
rs1938301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938303	0.98[ASN][1000 genomes]
rs1938304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938407	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2088956	0.97[ASN][1000 genomes]
rs2105458	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2186219	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2356302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs238249	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2997458	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2997461	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2997465	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3009968	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3009969	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3009974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3009979	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3121732	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3121769	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34134455	0.98[ASN][1000 genomes]
rs346684	0.98[ASN][1000 genomes]
rs346687	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346693	0.98[ASN][1000 genomes]
rs346695	0.98[ASN][1000 genomes]
rs346696	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346697	0.98[ASN][1000 genomes]
rs346698	0.98[ASN][1000 genomes]
rs346700	0.98[ASN][1000 genomes]
rs346701	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346702	0.98[ASN][1000 genomes]
rs346705	0.98[ASN][1000 genomes]
rs346706	0.98[ASN][1000 genomes]
rs346707	0.98[ASN][1000 genomes]
rs346708	0.91[ASN][1000 genomes]
rs346712	0.98[ASN][1000 genomes]
rs346716	0.98[ASN][1000 genomes]
rs346717	0.98[ASN][1000 genomes]
rs346719	0.98[ASN][1000 genomes]
rs346721	0.98[ASN][1000 genomes]
rs346723	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346724	0.98[ASN][1000 genomes]
rs346729	0.98[ASN][1000 genomes]
rs346731	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346732	0.98[ASN][1000 genomes]
rs346733	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346734	0.98[ASN][1000 genomes]
rs346735	0.98[ASN][1000 genomes]
rs346736	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346737	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738246	0.97[ASN][1000 genomes]
rs3850855	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850856	0.98[ASN][1000 genomes]
rs415536	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4454584	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs454624	0.98[ASN][1000 genomes]
rs4660295	0.98[ASN][1000 genomes]
rs4660834	0.97[ASN][1000 genomes]
rs4660839	0.98[ASN][1000 genomes]
rs4660841	0.98[ASN][1000 genomes]
rs56363452	0.98[ASN][1000 genomes]
rs56791336	0.98[ASN][1000 genomes]
rs58374842	0.98[ASN][1000 genomes]
rs58934647	0.98[ASN][1000 genomes]
rs59220391	0.89[ASN][1000 genomes]
rs61789780	0.98[ASN][1000 genomes]
rs61789781	0.98[ASN][1000 genomes]
rs6429557	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688318	0.97[ASN][1000 genomes]
rs6702327	0.97[ASN][1000 genomes]
rs72684493	0.98[ASN][1000 genomes]
rs974143	0.98[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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	esv3365432	chr1:45670715-45673638	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3444099	chr1:45670790-45673738	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45668000-45673800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:45668600-45672800	Active TSS	Fetal Brain Female	brain
3	chr1:45669400-45673200	Active TSS	Brain Angular Gyrus	brain
4	chr1:45669400-45673400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:45670000-45672800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:45670000-45673200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:45670000-45673400	Active TSS	Ovary	ovary
8	chr1:45670200-45672800	Active TSS	Rectal Smooth Muscle	rectum
9	chr1:45670400-45673200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:45670600-45672800	Active TSS	NHLF	lung
11	chr1:45670600-45673000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:45670600-45673000	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr1:45670600-45673200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:45670600-45673200	Active TSS	Colonic Mucosa	Colon
15	chr1:45670800-45672800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:45670800-45672800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:45670800-45672800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:45670800-45672800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:45670800-45672800	Active TSS	Fetal Kidney	kidney
20	chr1:45670800-45672800	Bivalent/Poised TSS	HepG2	liver
21	chr1:45670800-45673000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr1:45670800-45673000	Active TSS	Pancreas	Pancrea
23	chr1:45671000-45672800	Active TSS	Small Intestine	intestine
24	chr1:45671000-45672800	Bivalent/Poised TSS	Thymus	Thymus
25	chr1:45671000-45673000	Active TSS	Aorta	Aorta
26	chr1:45671000-45673000	Active TSS	Right Ventricle	heart
27	chr1:45671200-45672800	Active TSS	Colon Smooth Muscle	Colon
28	chr1:45671200-45672800	Active TSS	Gastric	stomach
29	chr1:45671200-45672800	Active TSS	Lung	lung
30	chr1:45671200-45673000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:45671200-45673000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:45671200-45673000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:45671200-45673000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr1:45671200-45673200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:45671400-45672800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:45671400-45673000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr1:45671400-45673200	Active TSS	Brain Germinal Matrix	brain
38	chr1:45671400-45673200	Active TSS	Fetal Intestine Large	intestine
39	chr1:45671600-45673000	Flanking Bivalent TSS/Enh	Dnd41	blood
40	chr1:45671800-45672800	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
41	chr1:45672200-45673000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
42	chr1:45672400-45672800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:45672400-45672800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
44	chr1:45672400-45672800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
45	chr1:45672400-45672800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
46	chr1:45672400-45672800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:45672400-45672800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:45672400-45672800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:45672400-45672800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
50	chr1:45672400-45672800	Flanking Bivalent TSS/Enh	HSMM	muscle

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