Variant report

Variant	rs3753872
Chromosome Location	chr1:95699184-95699185
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:95699181-95699185	K562	blood:	n/a	n/a
2	TBP	chr1:95699104-95700246	K562	blood:	n/a	n/a
3	RCOR1	chr1:95698181-95700584	IMR90	lung:	n/a	n/a
4	MAX	chr1:95699088-95700077	GM12878	blood:	n/a	n/a
5	FOXA1	chr1:95698695-95699271	HepG2	liver:	n/a	n/a
6	MAZ	chr1:95698762-95700551	IMR90	lung:	n/a	chr1:95700157-95700167
7	YY1	chr1:95698793-95699188	HepG2	liver:	n/a	n/a
8	HNF4A	chr1:95698799-95699227	HepG2	liver:	n/a	n/a
9	MYBL2	chr1:95698744-95700030	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:95698945-95700437	K562	blood:	n/a	n/a
11	POLR2A	chr1:95699142-95700142	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:95698513-95700286	HepG2	liver:	n/a	n/a
13	TBP	chr1:95698748-95699939	HepG2	liver:	n/a	n/a
14	RCOR1	chr1:95698346-95699995	K562	blood:	n/a	n/a
15	MXI1	chr1:95698789-95700296	HepG2	liver:	n/a	n/a
16	RAD21	chr1:95699032-95700729	SK-N-SH	brain:	n/a	chr1:95700083-95700096
17	MAZ	chr1:95699147-95700095	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:95699138-95700205	PFSK-1	brain:	n/a	n/a
19	TAF1	chr1:95699180-95700105	A549	lung:	n/a	n/a
20	SIN3A	chr1:95698856-95700125	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXA1	chr1:95698779-95699216	HepG2	liver:	n/a	n/a
22	SMARCB1	chr1:95698873-95700221	Hela-S3	cervix:	n/a	n/a
23	HNF4A	chr1:95698770-95699845	HepG2	liver:	n/a	n/a
24	MYBL2	chr1:95698646-95699443	HepG2	liver:	n/a	n/a
25	RAD21	chr1:95699089-95699972	IMR90	lung:	n/a	n/a
26	ZNF143	chr1:95699070-95700001	H1-hESC	embryonic stem cell:	n/a	chr1:95699098-95699117
27	MBD4	chr1:95698921-95699295	HepG2	liver:	n/a	n/a
28	HCFC1	chr1:95699096-95700306	Hela-S3	cervix:	n/a	n/a
29	UBTF	chr1:95698513-95700160	K562	blood:	n/a	n/a
30	POLR2A	chr1:95698730-95699266	HepG2	liver:	n/a	n/a
31	MAX	chr1:95698656-95700220	A549	lung:	n/a	chr1:95700157-95700167
32	CTCF	chr1:95698580-95700135	A549	lung:	n/a	n/a
33	FOXA1	chr1:95698731-95699302	HepG2	liver:	n/a	n/a
34	TCF7L2	chr1:95699168-95699973	Hela-S3	cervix:	n/a	n/a
35	SMC3	chr1:95699168-95700515	SK-N-SH	brain:	n/a	chr1:95700035-95700045
36	ELF1	chr1:95698929-95700264	GM12878	blood:	n/a	chr1:95700118-95700130 chr1:95700015-95700027
37	JUND	chr1:95698395-95700007	K562	blood:	n/a	n/a
38	RCOR1	chr1:95698903-95700042	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:95698717-95700234	HepG2	liver:	n/a	n/a
40	HEY1	chr1:95698751-95699251	HepG2	liver:	n/a	n/a
41	EP300	chr1:95698775-95699208	HepG2	liver:	n/a	n/a
42	HEY1	chr1:95698664-95699317	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:95698843-95700058	PBDE	blood:	n/a	n/a
44	RCOR1	chr1:95699006-95700018	K562	blood:	n/a	n/a
45	MAZ	chr1:95698917-95699200	HepG2	liver:	n/a	n/a
46	NRF1	chr1:95699045-95699244	GM12878	blood:	n/a	n/a
47	CTBP2	chr1:95698933-95699968	H1-hESC	embryonic stem cell:	n/a	n/a
48	SMARCC1	chr1:95699093-95700119	Hela-S3	cervix:	n/a	n/a
49	MAX	chr1:95698787-95700470	K562	blood:	n/a	chr1:95700157-95700167
50	CHD2	chr1:95698962-95699914	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:95581571..95584597-chr1:95698513..95700535,3	MCF-7	breast:
2	chr1:95582616..95585939-chr1:95698259..95700506,4	K562	blood:
3	chr1:95536810..95539827-chr1:95698878..95701315,3	K562	blood:
4	chr1:95582556..95585358-chr1:95698094..95701319,5	K562	blood:

No data

Variant related genes	Relation type
RWDD3	TF binding region
ENSG00000231992	Chromatin interaction
ENSG00000152078	Chromatin interaction
ENSG00000271092	Chromatin interaction
ENSG00000172339	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10874906	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10874908	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165314	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs11165318	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11165319	0.81[ASN][1000 genomes]
rs11165333	0.92[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11165343	0.94[ASN][1000 genomes]
rs11165346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11165349	1.00[ASN][1000 genomes]
rs12034397	0.99[ASN][1000 genomes]
rs12036706	0.81[ASN][1000 genomes]
rs12037572	0.93[ASN][1000 genomes]
rs12048133	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12084387	0.93[CHB][hapmap]
rs12085822	0.81[ASN][1000 genomes]
rs12401359	1.00[ASN][1000 genomes]
rs12407571	0.81[ASN][1000 genomes]
rs12408858	0.95[ASN][1000 genomes]
rs1927043	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2147587	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2148797	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2296308	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs259341	0.98[ASN][1000 genomes]
rs259342	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs259344	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259348	0.98[ASN][1000 genomes]
rs259351	0.99[ASN][1000 genomes]
rs259353	0.99[ASN][1000 genomes]
rs259356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3738170	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738171	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767313	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767315	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820345	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4950024	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547339	1.00[ASN][1000 genomes]
rs564610	0.98[ASN][1000 genomes]
rs592097	0.99[ASN][1000 genomes]
rs61771764	0.92[ASN][1000 genomes]
rs61771765	0.94[ASN][1000 genomes]
rs61771766	0.94[ASN][1000 genomes]
rs658018	0.99[ASN][1000 genomes]
rs6666528	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6671408	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702139	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs688633	0.98[ASN][1000 genomes]
rs7528790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3753872	RWDD3	cis	Muscle Skeletal	GTEx
rs3753872	RWDD3	cis	multi-tissue	Pritchard
rs3753872	ALG14	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95698200-95699200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:95698200-95699200	Flanking Active TSS	Brain Cingulate Gyrus	brain
3	chr1:95698200-95699400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:95698200-95699400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:95698200-95699400	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr1:95698200-95699400	Flanking Active TSS	Fetal Lung	lung
7	chr1:95698200-95699400	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr1:95698200-95699400	Flanking Active TSS	K562	blood
9	chr1:95698200-95699400	Flanking Active TSS	Osteobl	bone
10	chr1:95698200-95699600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:95698200-95699600	Flanking Active TSS	Liver	Liver
12	chr1:95698200-95700400	Active TSS	Aorta	Aorta
13	chr1:95698200-95700600	Active TSS	Colon Smooth Muscle	Colon
14	chr1:95698200-95700600	Active TSS	Ovary	ovary
15	chr1:95698200-95700600	Active TSS	Right Atrium	heart
16	chr1:95698200-95700600	Active TSS	A549	lung
17	chr1:95698400-95699200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:95698400-95699400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:95698400-95699400	Flanking Active TSS	HMEC	breast
20	chr1:95698400-95700400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:95698400-95700600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:95698400-95700600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:95698400-95700600	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:95698400-95700600	Active TSS	Fetal Kidney	kidney
25	chr1:95698400-95700600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:95698600-95699200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr1:95698600-95699200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr1:95698600-95699200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:95698600-95699200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:95698600-95699200	Flanking Active TSS	Fetal Heart	heart
31	chr1:95698600-95699400	Flanking Active TSS	HSMMtube	muscle
32	chr1:95698600-95699400	Flanking Active TSS	HUVEC	blood vessel
33	chr1:95698600-95700400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr1:95698600-95700600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:95698600-95700600	Active TSS	Brain Anterior Caudate	brain
36	chr1:95698600-95700600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:95698600-95700600	Active TSS	Fetal Intestine Large	intestine
38	chr1:95698600-95700600	Active TSS	Right Ventricle	heart
39	chr1:95698600-95700600	Active TSS	NHDF-Ad	bronchial
40	chr1:95698800-95699200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr1:95698800-95699200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr1:95698800-95699200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:95698800-95699200	Flanking Active TSS	Fetal Brain Male	brain
44	chr1:95698800-95699200	Flanking Active TSS	Lung	lung
45	chr1:95698800-95699400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:95698800-95699400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:95698800-95699400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:95698800-95699400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:95698800-95699400	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr1:95698800-95699400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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