Variant report

Variant	rs6721593
Chromosome Location	chr2:55630729-55630730
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:55630552-55630803	HepG2	liver:	n/a	n/a
2	MAFF	chr2:55630533-55630781	HepG2	liver:	n/a	chr2:55630666-55630684

No.	Distal block	Cell Line	Cell type
1	chr2:55624788..55628704-chr2:55629085..55632054,3	K562	blood:
2	chr2:55629328..55632200-chr2:55634808..55637417,2	K562	blood:
3	chr2:55629189..55632200-chr2:55632234..55637417,4	K562	blood:
4	chr2:55627338..55628874-chr2:55629453..55631312,2	MCF-7	breast:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10182704	0.90[EUR][1000 genomes]
rs10184756	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10198652	1.00[YRI][hapmap]
rs10454144	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125565	0.90[EUR][1000 genomes]
rs11125566	0.90[EUR][1000 genomes]
rs11125568	0.84[JPT][hapmap]
rs11125569	0.84[JPT][hapmap]
rs11125572	0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12612806	0.93[EUR][1000 genomes]
rs12617891	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs12618216	0.90[ASN][1000 genomes]
rs12618795	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes]
rs12623954	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713297	0.84[ASN][1000 genomes]
rs13416912	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1454415	1.00[ASN][1000 genomes]
rs1454419	0.98[ASN][1000 genomes]
rs1454420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1454423	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1454424	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545554	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs17735450	1.00[CEU][hapmap]
rs1902056	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902057	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs1902058	0.93[EUR][1000 genomes]
rs1902061	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1902062	0.80[ASN][1000 genomes]
rs2043713	1.00[YRI][hapmap]
rs2045132	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs2045133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045134	0.98[ASN][1000 genomes]
rs2045135	1.00[ASN][1000 genomes]
rs2045136	0.93[ASN][1000 genomes]
rs2123983	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2219130	0.93[EUR][1000 genomes]
rs2576688	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2576703	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589057	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589068	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589069	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589070	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589078	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589079	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589104	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2864831	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs2864832	0.90[EUR][1000 genomes]
rs2867173	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2867178	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs2867179	0.93[EUR][1000 genomes]
rs2867194	0.82[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2902857	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs2903507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2903509	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2903514	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917777	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2920963	1.00[YRI][hapmap]
rs2920970	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs2966466	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs3099080	0.90[EUR][1000 genomes]
rs3099081	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3099083	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs3111408	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3111409	0.88[EUR][1000 genomes]
rs3748943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3974263	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233960	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233961	0.82[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277563	1.00[ASN][1000 genomes]
rs4481025	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4535081	0.93[EUR][1000 genomes]
rs4672030	0.81[EUR][1000 genomes]
rs4672032	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4672033	0.93[EUR][1000 genomes]
rs4672035	0.83[JPT][hapmap]
rs4672036	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4672037	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4672038	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672040	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4672041	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672043	0.91[ASN][1000 genomes]
rs4672044	0.91[ASN][1000 genomes]
rs59634508	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61157332	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6545489	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs6545490	0.82[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545491	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545492	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6709204	0.82[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs6710192	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6718031	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6718909	0.90[EUR][1000 genomes]
rs6720698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6724840	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs6725968	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs6732633	0.91[ASN][1000 genomes]
rs6732759	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6733814	1.00[ASN][1000 genomes]
rs6744426	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6748979	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72924907	0.90[EUR][1000 genomes]
rs7424286	0.96[ASN][1000 genomes]
rs7557555	0.88[EUR][1000 genomes]
rs7557956	0.89[EUR][1000 genomes]
rs7559987	0.84[JPT][hapmap]
rs7579037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7586440	0.82[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs7595396	0.82[AMR][1000 genomes]
rs7601588	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs7602189	1.00[ASN][1000 genomes]
rs7606361	0.82[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv275364	chr2:55621732-55632233	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
4	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
8	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
13	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:55600600-55631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
19	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
20	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:55616600-55635400	Weak transcription	HMEC	breast
22	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
23	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
24	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
25	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
27	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:55619000-55632200	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:55619600-55632000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:55623000-55635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
33	chr2:55623600-55632200	Weak transcription	GM12878-XiMat	blood
34	chr2:55624200-55635600	Weak transcription	NHEK	skin
35	chr2:55624400-55645600	Weak transcription	Ovary	ovary
36	chr2:55624600-55632600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:55627000-55631400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:55627600-55630800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:55627800-55636000	Weak transcription	NHDF-Ad	bronchial
40	chr2:55628000-55632200	Weak transcription	NHLF	lung
41	chr2:55628200-55633000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:55628400-55632200	Weak transcription	Left Ventricle	heart
43	chr2:55628600-55631000	Enhancers	Brain Hippocampus Middle	brain
44	chr2:55628600-55632600	Weak transcription	Fetal Intestine Small	intestine
45	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
46	chr2:55629000-55631600	Weak transcription	HepG2	liver
47	chr2:55629000-55634400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:55629000-55635600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:55629200-55632200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:55629400-55631000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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