Variant report

Variant	rs2689679
Chromosome Location	chr1:77685683-77685684
allele	C/G
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	FOS	chr1:77685554-77685785	MCF10A-Er-Src	breast:	n/a	n/a
2	ARID3A	chr1:77685466-77685797	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:77684293-77685770	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:77684794-77685685	HEK293	kidney:	n/a	n/a
5	MAX	chr1:77684299-77685736	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:77684194-77685806	Hela-S3	cervix:	n/a	n/a
7	ZMIZ1	chr1:77684693-77685711	K562	blood:	n/a	n/a
8	GTF2F1	chr1:77684546-77685725	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:77684671-77685876	PBDE	blood:	n/a	n/a
10	HCFC1	chr1:77683952-77686153	Hela-S3	cervix:	n/a	n/a
11	RAD21	chr1:77684263-77685830	IMR90	lung:	n/a	chr1:77685187-77685196
12	STAT3	chr1:77684974-77685916	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:77685591-77685711	HepG2	liver:	n/a	n/a
14	CHD1	chr1:77684827-77685690	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr1:77683938-77686114	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

Variant related genes	Relation type
PIGK	TF binding region
ENSG00000154027	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1098121	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1098129	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1098132	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1098133	0.84[AFR][1000 genomes]
rs1103683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1253224	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253226	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1266316	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs1270993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723684	0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs12744696	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12746974	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1419249	0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs1502526	0.91[JPT][hapmap]
rs1502533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1615806	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs17099885	0.90[JPT][hapmap]
rs17099982	0.90[JPT][hapmap]
rs17099983	0.90[JPT][hapmap]
rs17099986	0.91[JPT][hapmap]
rs17100001	0.91[JPT][hapmap]
rs17100002	0.90[JPT][hapmap]
rs17100005	0.91[JPT][hapmap]
rs17100021	0.91[JPT][hapmap]
rs17100026	0.90[JPT][hapmap]
rs1721127	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1721140	0.84[AFR][1000 genomes]
rs1721145	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs1721151	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs1779174	0.85[AFR][1000 genomes]
rs1779186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779189	0.84[AFR][1000 genomes]
rs1779198	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs2653469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2689666	0.82[AFR][1000 genomes]
rs2689674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2689675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2689678	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762882	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs2799564	0.97[YRI][hapmap];0.94[AFR][1000 genomes]
rs35446093	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67263641	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71658787	0.94[AFR][1000 genomes]
rs72681896	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7524360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs839799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs839808	0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs839810	0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs839814	0.90[AFR][1000 genomes]
rs839818	0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs839820	0.90[JPT][hapmap]
rs839821	0.89[JPT][hapmap]
rs839822	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs839823	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs839824	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];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs839826	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs839827	0.85[AFR][1000 genomes]
rs839830	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs839831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77682800-77686400	Active TSS	GM12878-XiMat	blood
2	chr1:77683600-77686200	Active TSS	K562	blood
3	chr1:77683800-77686000	Active TSS	NHLF	lung
4	chr1:77683800-77686200	Active TSS	A549	lung
5	chr1:77684000-77685800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:77684000-77685800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:77684000-77686000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:77684000-77686000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr1:77684000-77686000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:77684000-77686000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:77684000-77686000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr1:77684000-77686000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr1:77684000-77686000	Active TSS	Thymus	Thymus
14	chr1:77684000-77686200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:77684000-77686200	Active TSS	NHDF-Ad	bronchial
18	chr1:77684000-77686600	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:77684200-77685800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:77684200-77685800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:77684200-77685800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:77684200-77685800	Active TSS	Fetal Stomach	stomach
23	chr1:77684200-77685800	Active TSS	Left Ventricle	heart
24	chr1:77684200-77685800	Active TSS	Placenta Amnion	Placenta Amnion
25	chr1:77684200-77685800	Active TSS	Psoas Muscle	Psoas
26	chr1:77684200-77685800	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:77684200-77685800	Active TSS	Right Atrium	heart
28	chr1:77684200-77685800	Active TSS	Hela-S3	cervix
29	chr1:77684200-77685800	Active TSS	HSMMtube	muscle
30	chr1:77684200-77685800	Active TSS	NHEK	skin
31	chr1:77684200-77686000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:77684200-77686000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:77684200-77686000	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:77684200-77686000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:77684200-77686000	Active TSS	Brain Germinal Matrix	brain
36	chr1:77684200-77686000	Active TSS	Fetal Intestine Large	intestine
37	chr1:77684200-77686000	Active TSS	Fetal Intestine Small	intestine
38	chr1:77684200-77686000	Active TSS	Fetal Kidney	kidney
39	chr1:77684200-77686000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr1:77684200-77686000	Active TSS	Fetal Muscle Leg	muscle
41	chr1:77684200-77686000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr1:77684200-77686000	Active TSS	Stomach Smooth Muscle	stomach
43	chr1:77684200-77686200	Active TSS	HMEC	breast
44	chr1:77684200-77686400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr1:77684200-77686400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:77684400-77685800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr1:77684400-77685800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:77684400-77685800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:77684400-77685800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:77684400-77685800	Active TSS	Primary T cells fromperipheralblood	blood

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