Variant report

Variant	rs7551211
Chromosome Location	chr1:78003085-78003086
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	STAT3	chr1:78002944-78003225	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr1:78002124-78003540	SK-N-SH	brain:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
3	FOSL2	chr1:78002159-78003161	SK-N-SH	brain:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
4	GATA2	chr1:78002332-78003255	HUVEC	blood vessel:	n/a	chr1:78002858-78002868
5	CTCF	chr1:78002960-78003110	HMF	breast:	n/a	n/a
6	NFIC	chr1:78002037-78003143	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:78002245-78003295	U87	brain:	n/a	n/a
8	JUND	chr1:78002193-78003185	HCT-116	colon:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
9	PBX3	chr1:78002269-78003333	SK-N-SH	brain:	n/a	n/a
10	JUND	chr1:78002194-78003135	SK-N-SH	brain:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
11	POLR2A	chr1:78002145-78003301	U87	brain:	n/a	n/a
12	MAX	chr1:78002344-78003095	A549	lung:	n/a	n/a
13	CTCF	chr1:78002940-78003090	BJ	skin:	n/a	n/a
14	TEAD4	chr1:78002126-78003155	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr1:78002215-78003096	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:78002256-78003462	U87	brain:	n/a	n/a
17	RXRA	chr1:78002271-78003116	SK-N-SH	brain:	n/a	n/a
18	GATA3	chr1:78002131-78003335	SK-N-SH	brain:	n/a	chr1:78002858-78002868
19	SP1	chr1:78002163-78003220	HCT-116	colon:	n/a	n/a
20	GATA3	chr1:78002153-78003406	SK-N-SH	brain:	n/a	chr1:78002858-78002868
21	TCF12	chr1:78002101-78003255	SK-N-SH	brain:	n/a	n/a
22	TCF12	chr1:78002148-78003260	SK-N-SH	brain:	n/a	n/a
23	JUND	chr1:78002246-78003196	SK-N-SH	brain:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
24	JUND	chr1:78002219-78003098	HCT-116	colon:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
25	FOSL2	chr1:78002181-78003113	A549	lung:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
26	CBX3	chr1:78002310-78003153	HCT-116	colon:	n/a	n/a
27	MAX	chr1:78002321-78003092	SK-N-SH	brain:	n/a	n/a
28	EP300	chr1:78002139-78003180	SK-N-SH	brain:	n/a	n/a
29	TCF7L2	chr1:78002496-78003085	Hela-S3	cervix:	n/a	chr1:78002803-78002812 chr1:78002800-78002816 chr1:78002800-78002816 chr1:78002607-78002616 chr1:78002802-78002812 chr1:78002801-78002815
30	PBX3	chr1:78002232-78003345	SK-N-SH	brain:	n/a	n/a
31	FOSL1	chr1:78002161-78003155	HCT-116	colon:	n/a	chr1:78002607-78002615 chr1:78002606-78002616 chr1:78002606-78002616 chr1:78002605-78002617 chr1:78002606-78002616
32	POLR2A	chr1:78002256-78003405	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78000743..78003478-chr1:78147875..78150307,2	MCF-7	breast:

Variant related genes	Relation type
AK5	TF binding region
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1013399	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782654	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873949	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873950	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10873951	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11162362	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162364	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162365	0.90[ASN][1000 genomes]
rs11162369	0.83[ASN][1000 genomes]
rs11162372	0.81[ASN][1000 genomes]
rs12071212	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074409	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12095064	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142671	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs12717767	0.90[ASN][1000 genomes]
rs12724560	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565850	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565851	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1565852	0.86[ASN][1000 genomes]
rs1962523	0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1976334	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029768	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133202	0.90[ASN][1000 genomes]
rs2172727	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2647486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647487	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278854	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs2803136	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2803168	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34773766	0.89[ASN][1000 genomes]
rs3509	0.89[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs371076	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs3738079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767030	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap]
rs3767032	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767033	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4245658	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4589153	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600093	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949657	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949658	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949659	0.89[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949807	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949808	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949809	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4949811	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4949813	0.91[ASN][1000 genomes]
rs4949816	0.94[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs6603952	0.80[ASN][1000 genomes]
rs6603953	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6603955	0.90[ASN][1000 genomes]
rs6667519	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs6667803	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675743	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6692369	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695989	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696083	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs728741	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7513619	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7519476	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524147	0.94[ASN][1000 genomes]
rs7524866	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7531286	0.82[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545544	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872342	0.83[CHD][hapmap]
rs962388	0.91[ASN][1000 genomes]
rs9787153	0.92[EUR][1000 genomes];1.00[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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7551211	AK5	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:77998200-78005000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:77999200-78004600	Enhancers	NH-A	brain
5	chr1:77999600-78003800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:77999600-78004000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:77999600-78009600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:77999800-78005200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:78000000-78003600	Weak transcription	Liver	Liver
10	chr1:78000000-78003800	Genic enhancers	NHDF-Ad	bronchial
11	chr1:78000000-78004400	Weak transcription	Fetal Kidney	kidney
12	chr1:78000000-78005000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:78000000-78011600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:78000200-78004600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:78000200-78004600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:78000200-78004600	Weak transcription	Brain Substantia Nigra	brain
19	chr1:78000200-78005000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:78000200-78005000	Weak transcription	Brain Anterior Caudate	brain
21	chr1:78000800-78006800	Strong transcription	Primary T cells from cord blood	blood
22	chr1:78001000-78004800	Enhancers	Hela-S3	cervix
23	chr1:78001000-78004800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:78001000-78005000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:78001200-78004600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:78001400-78003800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:78001400-78004000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:78001400-78004800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:78001400-78006600	Enhancers	NHEK	skin
30	chr1:78001600-78005000	Enhancers	HSMM	muscle
31	chr1:78001600-78005800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:78001600-78006200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:78001600-78006600	Enhancers	HMEC	breast
34	chr1:78001800-78006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:78002000-78003400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:78002000-78003400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr1:78002000-78003600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:78002000-78003600	Strong transcription	Brain Hippocampus Middle	brain
39	chr1:78002000-78003800	Enhancers	HUVEC	blood vessel
40	chr1:78002000-78004800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:78002200-78003200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:78002200-78004400	Enhancers	A549	lung
43	chr1:78002200-78004600	Enhancers	HSMMtube	muscle
44	chr1:78002200-78004600	Enhancers	Osteobl	bone
45	chr1:78002200-78005200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:78002400-78003200	Genic enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:78002400-78004800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:78002400-78004800	Enhancers	NHLF	lung
49	chr1:78002800-78003200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:78002800-78003200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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