Variant report

Variant	rs59556963
Chromosome Location	chr3:194877126-194877127
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:194874776-194877542	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:194877083-194877339	HUVEC	blood vessel:	n/a	n/a
3	FOS	chr3:194876644-194877264	HUVEC	blood vessel:	n/a	chr3:194876814-194876826 chr3:194877152-194877161 chr3:194876815-194876825 chr3:194876815-194876825 chr3:194876815-194876825 chr3:194876817-194876828 chr3:194876815-194876824 chr3:194876815-194876825
4	POLR2A	chr3:194874381-194877258	HUVEC	blood vessel:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:194877106-194877156	Hela-S3	cervix:	n/a
2	chr3:194877106-194877156	MCF10A-Er-Src	breast:	n/a
3	chr3:194877106-194877156	K562	blood:	n/a
4	chr3:194877106-194877156	HL-60	blood:	n/a
5	chr3:194877106-194877156	NB4	blood:	n/a
6	chr3:194877106-194877156	HMEC	breast:	n/a
7	chr3:194877106-194877156	GM19239	blood:	n/a
8	chr3:194877106-194877156	PrEC	prostate:	n/a
9	chr3:194877106-194877156	HEK293	kidney:	embryo
10	chr3:194877106-194877156	A549	lung:	n/a
11	chr3:194877106-194877156	HCM	heart:	n/a
12	chr3:194877106-194877156	ProgFib	skin:	n/a
13	chr3:194877106-194877156	ovcar-3	ovarian:	n/a
14	chr3:194877106-194877156	AoSMC	blood vessel:	n/a
15	chr3:194877106-194877156	AG10803	skin:	n/a
16	chr3:194877106-194877156	HPAEpiC	pulmonary alveolar:	n/a
17	chr3:194877106-194877156	HRE	kidney:	n/a
18	chr3:194877106-194877156	Caco-2	colon:	n/a
19	chr3:194877106-194877156	SAEC	small airway:	n/a
20	chr3:194877106-194877156	HCT-116	colon:	n/a
21	chr3:194877106-194877156	HAEpiC	amniotic membrane:	n/a
22	chr3:194877106-194877156	GM12891	blood:	n/a
23	chr3:194877106-194877156	H1-hESC	embryonic stem cell:	embryo
24	chr3:194877106-194877156	HepG2	liver:	n/a
25	chr3:194877106-194877156	HCPEpiC	choroid plexus:	n/a
26	chr3:194877106-194877156	T-47D	breast:	n/a
27	chr3:194877106-194877156	AG04449	skin:	fetal
28	chr3:194877106-194877156	HRPEpiC	eye:	n/a
29	chr3:194877106-194877156	NT2-D1	testis:	n/a
30	chr3:194877106-194877156	PANC-1	pancreas:	n/a
31	chr3:194877106-194877156	Hepatocyte	liver:	n/a
32	chr3:194877106-194877156	AG09319	gingival:	n/a
33	chr3:194877106-194877156	AG04450	lung:	fetal
34	chr3:194877106-194877156	RPTEC	kidney:	n/a
35	chr3:194877106-194877156	GM06990	blood:	n/a
36	chr3:194877106-194877156	SK-N-SH_RA	brain:	n/a
37	chr3:194877106-194877156	ECC-1	luminal epithelium:	n/a
38	chr3:194877106-194877156	HRCEpiC	kidney:	n/a
39	chr3:194877106-194877156	U87	brain:	n/a
40	chr3:194877106-194877156	NHDF-neo	bronchial:	n/a
41	chr3:194877106-194877156	LNCaP	prostate:	n/a
42	chr3:194877106-194877156	BE2_C	brain:	n/a
43	chr3:194877106-194877156	AG09309	skin:	n/a
44	chr3:194877106-194877156	PFSK-1	brain:	n/a
45	chr3:194877106-194877156	HUVEC	blood vessel:	n/a
46	chr3:194877106-194877156	SK-N-SH	brain:	n/a
47	chr3:194877106-194877156	CMK	blood:	n/a
48	chr3:194877106-194877156	HIPEpiC	eye:	n/a
49	chr3:194877106-194877156	SK-N-MC	brain:	n/a
50	chr3:194877106-194877156	GM12892	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:194865591..194868396-chr3:194874419..194877392,2	K562	blood:
2	chr3:194862609..194865401-chr3:194875415..194878786,3	K562	blood:
3	chr3:194837632..194840596-chr3:194875671..194877236,2	K562	blood:

No data

Variant related genes	Relation type
XXYLT1	TF binding region
XXYLT1	CpG island
ENSG00000244314	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10433328	0.89[ASN][1000 genomes]
rs10433329	0.93[ASN][1000 genomes]
rs10433330	0.93[ASN][1000 genomes]
rs10933700	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10933701	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491661	0.90[ASN][1000 genomes]
rs12491663	0.84[ASN][1000 genomes]
rs2004553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2088040	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2088041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2410844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2410846	0.81[ASN][1000 genomes]
rs28613110	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4677662	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677811	0.93[ASN][1000 genomes]
rs4677814	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59834989	0.82[AMR][1000 genomes]
rs60528401	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6437460	0.90[ASN][1000 genomes]
rs6799346	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73206648	0.88[ASN][1000 genomes]
rs73206650	0.88[ASN][1000 genomes]
rs73206651	0.93[ASN][1000 genomes]
rs750470	0.88[AFR][1000 genomes]
rs7628775	0.83[ASN][1000 genomes]
rs7637593	0.83[ASN][1000 genomes]
rs7653355	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903309	0.88[ASN][1000 genomes]
rs903311	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9809570	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9824084	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9825521	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
17	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
2	chr3:194862400-194897800	Weak transcription	Dnd41	blood
3	chr3:194868200-194877800	Enhancers	Fetal Stomach	stomach
4	chr3:194868400-194877400	Enhancers	Fetal Heart	heart
5	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
6	chr3:194870800-194877600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:194871000-194877200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:194871000-194880800	Enhancers	HUVEC	blood vessel
9	chr3:194871400-194877800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:194871400-194887400	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:194871600-194877600	Enhancers	Fetal Intestine Large	intestine
12	chr3:194871600-194881200	Weak transcription	Liver	Liver
13	chr3:194871800-194878200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:194871800-194882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:194872000-194877200	Enhancers	Stomach Mucosa	stomach
16	chr3:194872000-194877400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:194872000-194882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:194872000-194883000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:194872000-194883000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:194872400-194877600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:194872800-194877400	Enhancers	Right Atrium	heart
22	chr3:194872800-194877600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:194873000-194877200	Enhancers	Ovary	ovary
24	chr3:194873000-194877600	Enhancers	Adipose Nuclei	Adipose
25	chr3:194873000-194877800	Enhancers	Left Ventricle	heart
26	chr3:194873000-194884400	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:194873000-194884600	Enhancers	Fetal Thymus	thymus
28	chr3:194873600-194877400	Enhancers	Right Ventricle	heart
29	chr3:194873600-194877600	Enhancers	Colonic Mucosa	Colon
30	chr3:194873600-194877600	Enhancers	Fetal Muscle Trunk	muscle
31	chr3:194873800-194877200	Enhancers	Gastric	stomach
32	chr3:194873800-194877400	Enhancers	Fetal Brain Male	brain
33	chr3:194873800-194877400	Enhancers	Lung	lung
34	chr3:194873800-194877400	Enhancers	Pancreas	Pancrea
35	chr3:194873800-194879200	Enhancers	Spleen	Spleen
36	chr3:194874000-194877200	Enhancers	Psoas Muscle	Psoas
37	chr3:194874000-194877400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:194874000-194889800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:194874400-194879000	Enhancers	Primary B cells from cord blood	blood
40	chr3:194874600-194877600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr3:194875000-194877600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:194875200-194877600	Enhancers	Fetal Intestine Small	intestine
43	chr3:194875200-194879000	Enhancers	Thymus	Thymus
44	chr3:194875600-194877600	Enhancers	Fetal Lung	lung
45	chr3:194875800-194878800	Enhancers	GM12878-XiMat	blood
46	chr3:194876000-194877400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr3:194876000-194877600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:194876000-194880200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:194876200-194877200	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:194876200-194877400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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