Variant report

Variant	rs2297486
Chromosome Location	chr1:70688552-70688553
allele	A/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	CHD1	chr1:70686554-70688839	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr1:70688421-70688678	HepG2	liver:	n/a	chr1:70688562-70688575
3	STAT3	chr1:70688510-70688849	MCF10A-Er-Src	breast:	n/a	chr1:70688686-70688697 chr1:70688688-70688696
4	POLR2A	chr1:70686388-70698918	K562	blood:	n/a	n/a
5	STAT3	chr1:70688473-70689003	MCF10A-Er-Src	breast:	n/a	chr1:70688686-70688697 chr1:70688688-70688696
6	TBL1XR1	chr1:70687890-70688919	K562	blood:	n/a	n/a
7	IRF1	chr1:70688208-70688639	K562	blood:	n/a	n/a
8	STAT3	chr1:70688479-70688849	MCF10A-Er-Src	breast:	n/a	chr1:70688686-70688697 chr1:70688688-70688696
9	JUND	chr1:70688339-70688574	HepG2	liver:	n/a	chr1:70688424-70688433
10	JUN	chr1:70688394-70688717	HepG2	liver:	n/a	chr1:70688420-70688433 chr1:70688424-70688433

No.	Distal block	Cell Line	Cell type
1	chr1:70643607..70646837-chr1:70686224..70688710,3	K562	blood:
2	chr1:70688424..70691720-chr1:70692048..70694571,6	MCF-7	breast:
3	chr1:70668667..70673217-chr1:70684547..70688689,8	K562	blood:
4	chr1:70687323..70689346-chr1:70692516..70694332,3	MCF-7	breast:
5	chr1:70688440..70690850-chr1:70877083..70879333,2	K562	blood:
6	chr1:70686924..70688596-chr1:70820161..70821739,2	MCF-7	breast:
7	chr1:70667153..70674800-chr1:70681943..70693478,26	K562	blood:
8	chr1:70685268..70690578-chr1:70702989..70707451,6	MCF-7	breast:
9	chr1:70686799..70689606-chr1:70818481..70820974,3	K562	blood:
10	chr1:70686799..70688622-chr1:70819236..70822047,3	K562	blood:

Variant related genes	Relation type
ENSG00000228988	TF binding region
ENSG00000066557	Chromatin interaction
ENSG00000118454	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000244389	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10489927	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489928	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562802	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566666	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131235	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131251	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034756	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2210545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2478801	0.89[AMR][1000 genomes]
rs34821575	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35262515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753817	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767206	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767207	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767208	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41488747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs4649913	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650031	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55727788	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56902977	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639674	0.86[ASN][1000 genomes]
rs58696538	0.88[EUR][1000 genomes]
rs58927829	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59234513	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60272091	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60441970	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs632517	1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs655588	0.85[AMR][1000 genomes]
rs668525	1.00[MEX][hapmap];0.94[AMR][1000 genomes]
rs6702168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716240	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74085992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74088004	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088024	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088029	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74088032	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74088035	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088042	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7533067	0.82[CHD][hapmap]

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	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv871898	chr1:70681486-70723347	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297486	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70686200-70688600	Active TSS	Stomach Smooth Muscle	stomach
2	chr1:70686200-70689200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:70686400-70688600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:70686400-70688800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:70686400-70688800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:70686400-70688800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:70686400-70689000	Active TSS	Brain Germinal Matrix	brain
8	chr1:70686600-70688600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:70686600-70688600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:70686600-70688600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:70686600-70688600	Active TSS	Fetal Intestine Large	intestine
12	chr1:70686600-70688600	Active TSS	GM12878-XiMat	blood
13	chr1:70686600-70688600	Active TSS	NHLF	lung
14	chr1:70686600-70688800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr1:70686600-70688800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:70686600-70688800	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr1:70686600-70688800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:70686600-70688800	Active TSS	HSMMtube	muscle
19	chr1:70686600-70689000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:70686600-70689000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:70686600-70689000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:70686600-70689000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:70686600-70689000	Active TSS	A549	lung
24	chr1:70686600-70689000	Active TSS	HMEC	breast
25	chr1:70686600-70689200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:70686800-70688600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:70686800-70688600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:70686800-70688600	Active TSS	NHEK	skin
29	chr1:70686800-70689000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:70687000-70688600	Active TSS	Liver	Liver
31	chr1:70687000-70689000	Active TSS	NH-A	brain
32	chr1:70687400-70689000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:70687600-70688600	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr1:70687600-70688800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr1:70687600-70689600	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr1:70687800-70688800	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:70687800-70688800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr1:70687800-70688800	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:70687800-70688800	Active TSS	Right Atrium	heart
40	chr1:70687800-70689000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:70687800-70689000	Flanking Active TSS	Fetal Brain Female	brain
42	chr1:70687800-70689000	Flanking Active TSS	Fetal Heart	heart
43	chr1:70687800-70691200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:70687800-70697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:70687800-70698600	Weak transcription	Gastric	stomach
46	chr1:70687800-70698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:70687800-70699600	Weak transcription	Lung	lung
48	chr1:70687800-70699600	Weak transcription	Spleen	Spleen
49	chr1:70688000-70688600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:70688000-70688600	Weak transcription	Stomach Mucosa	stomach

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