Variant report

Variant	rs2765249
Chromosome Location	chr1:62729458-62729459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:62728932-62729548	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr1:62729012-62729504	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:62729423-62729473	HRE	kidney:	n/a
2	chr1:62729423-62729473	HNPCEpiC	eye:	n/a
3	chr1:62729423-62729473	RPTEC	kidney:	n/a
4	chr1:62729423-62729473	GM19239	blood:	n/a
5	chr1:62729423-62729473	SAEC	small airway:	n/a
6	chr1:62729423-62729473	AG04449	skin:	fetal
7	chr1:62729423-62729473	MCF-7	breast:	n/a
8	chr1:62729423-62729473	HRPEpiC	eye:	n/a
9	chr1:62729423-62729473	HEK293	kidney:	embryo
10	chr1:62729423-62729473	NB4	blood:	n/a
11	chr1:62729423-62729473	SKMC	muscle:	n/a
12	chr1:62729423-62729473	HCPEpiC	choroid plexus:	n/a
13	chr1:62729423-62729473	ovcar-3	ovarian:	n/a
14	chr1:62729423-62729473	BJ	skin:	n/a
15	chr1:62729423-62729473	HCF	heart:	n/a
16	chr1:62729423-62729473	K562	blood:	n/a
17	chr1:62729423-62729473	AG10803	skin:	n/a
18	chr1:62729423-62729473	NT2-D1	testis:	n/a
19	chr1:62729423-62729473	HIPEpiC	eye:	n/a
20	chr1:62729423-62729473	AG04450	lung:	fetal
21	chr1:62729423-62729473	Hepatocyte	liver:	n/a
22	chr1:62729423-62729473	PANC-1	pancreas:	n/a
23	chr1:62729423-62729473	PFSK-1	brain:	n/a
24	chr1:62729423-62729473	HL-60	blood:	n/a
25	chr1:62729423-62729473	U87	brain:	n/a
26	chr1:62729423-62729473	NHDF-neo	bronchial:	n/a
27	chr1:62729423-62729473	GM12878	blood:	n/a
28	chr1:62729423-62729473	T-47D	breast:	n/a
29	chr1:62729423-62729473	Hela-S3	cervix:	n/a
30	chr1:62729423-62729473	GM12891	blood:	n/a
31	chr1:62729423-62729473	SK-N-SH	brain:	n/a
32	chr1:62729423-62729473	NH-A	brain:	n/a
33	chr1:62729423-62729473	HCT-116	colon:	n/a
34	chr1:62729423-62729473	AG09319	gingival:	n/a
35	chr1:62729423-62729473	HEEpiC	esophagus:	n/a
36	chr1:62729423-62729473	ECC-1	luminal epithelium:	n/a
37	chr1:62729423-62729473	Caco-2	colon:	n/a
38	chr1:62729423-62729473	CMK	blood:	n/a
39	chr1:62729423-62729473	LNCaP	prostate:	n/a
40	chr1:62729423-62729473	HMEC	breast:	n/a
41	chr1:62729423-62729473	SK-N-MC	brain:	n/a
42	chr1:62729423-62729473	H1-hESC	embryonic stem cell:	embryo
43	chr1:62729423-62729473	ProgFib	skin:	n/a
44	chr1:62729423-62729473	IMR90	lung:	fetal
45	chr1:62729423-62729473	GM12892	blood:	n/a
46	chr1:62729423-62729473	MCF10A-Er-Src	breast:	n/a
47	chr1:62729423-62729473	HRCEpiC	kidney:	n/a
48	chr1:62729423-62729473	NHBE	bronchial:	n/a
49	chr1:62729423-62729473	SK-N-SH_RA	brain:	n/a
50	chr1:62729423-62729473	AoSMC	blood vessel:	n/a

No data

Variant related genes	Relation type
KANK4	TF binding region
KANK4	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12122645	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1806870	0.81[ASN][1000 genomes]
rs2258470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2260581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457806	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2457808	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2457810	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2457811	0.85[ASN][1000 genomes]
rs2666472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666473	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666474	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666475	0.99[ASN][1000 genomes]
rs2666476	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2666479	0.80[ASN][1000 genomes]
rs2666482	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2666503	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2666506	0.81[JPT][hapmap]
rs2666507	0.92[JPT][hapmap]
rs2666508	0.90[JPT][hapmap]
rs2765241	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765244	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765245	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765247	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765250	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2765270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6421473	0.81[ASN][1000 genomes]
rs7516290	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7529326	0.84[ASN][1000 genomes]
rs958803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9662717	0.84[ASN][1000 genomes]
rs982504	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62707600-62732000	Weak transcription	Gastric	stomach
2	chr1:62710800-62731800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:62711600-62730600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:62712000-62731600	Weak transcription	Placenta	Placenta
6	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:62727800-62729600	Strong transcription	HepG2	liver
8	chr1:62728000-62734800	Weak transcription	Fetal Brain Male	brain
9	chr1:62728600-62729600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:62728600-62729600	Enhancers	Fetal Heart	heart
11	chr1:62728600-62732000	Weak transcription	Fetal Kidney	kidney
12	chr1:62728800-62729600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:62728800-62729600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:62728800-62729600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr1:62728800-62729600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:62728800-62729600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:62728800-62729600	Enhancers	Adipose Nuclei	Adipose
18	chr1:62728800-62729600	Enhancers	Fetal Muscle Leg	muscle
19	chr1:62728800-62729800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr1:62728800-62730000	Genic enhancers	Fetal Stomach	stomach
21	chr1:62728800-62730400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:62729000-62729600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr1:62729000-62729600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:62729000-62729600	Enhancers	Fetal Lung	lung
25	chr1:62729000-62729800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:62729000-62737600	Weak transcription	Right Atrium	heart
27	chr1:62729200-62729600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr1:62729200-62731800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:62729200-62731800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:62729200-62732000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:62729400-62731800	Weak transcription	Liver	Liver
32	chr1:62729400-62731800	Weak transcription	Pancreas	Pancrea
33	chr1:62729400-62731800	Weak transcription	Spleen	Spleen
34	chr1:62729400-62732000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:62729400-62732600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:62729400-62734400	Strong transcription	Placenta Amnion	Placenta Amnion

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