Variant report

Variant	rs4656671
Chromosome Location	chr1:169336617-169336618
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	POLR2A	chr1:169336560-169338145	PBDE	blood:	n/a	n/a
2	POLR2A	chr1:169336275-169338640	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:169336612-169338063	HUVEC	blood vessel:	n/a	n/a
4	REST	chr1:169336277-169337717	H1-neurons	neurons:	n/a	n/a
5	SIN3AK20	chr1:169336555-169337893	MCF-7	breast:	n/a	n/a
6	MXI1	chr1:169336607-169337937	Hela-S3	cervix:	n/a	n/a
7	HCFC1	chr1:169336279-169338667	Hela-S3	cervix:	n/a	n/a
8	MAX	chr1:169336584-169337924	Hela-S3	cervix:	n/a	n/a
9	MYC	chr1:169336412-169337940	K562	blood:	n/a	chr1:169336502-169336511
10	GABPA	chr1:169336397-169338050	SK-N-SH	brain:	n/a	n/a
11	RCOR1	chr1:169336493-169338013	K562	blood:	n/a	n/a
12	SMC3	chr1:169336419-169337994	Hela-S3	cervix:	n/a	n/a
13	MAFK	chr1:169336574-169337583	Hela-S3	cervix:	n/a	n/a
14	MYC	chr1:169336426-169337597	MCF10A-Er-Src	breast:	n/a	chr1:169336502-169336511
15	MYC	chr1:169336544-169337857	MCF10A-Er-Src	breast:	n/a	n/a
16	RUNX3	chr1:169336597-169337776	GM12878	blood:	n/a	n/a
17	TFAP2C	chr1:169336450-169338078	Hela-S3	cervix:	n/a	chr1:169337154-169337169 chr1:169337420-169337429
18	EGR1	chr1:169336603-169337728	HCT-116	colon:	n/a	n/a
19	YY1	chr1:169336612-169337661	SK-N-SH	brain:	n/a	n/a
20	BHLHE40	chr1:169336436-169337888	K562	blood:	n/a	n/a
21	IRF1	chr1:169336597-169337836	K562	blood:	n/a	chr1:169337399-169337413 chr1:169337708-169337715 chr1:169337401-169337412 chr1:169337398-169337412 chr1:169336716-169336730 chr1:169337399-169337412 chr1:169336716-169336729 chr1:169337399-169337412 chr1:169336715-169336735
22	MXI1	chr1:169336053-169338642	IMR90	lung:	n/a	n/a
23	MAX	chr1:169336447-169337879	K562	blood:	n/a	chr1:169336502-169336511
24	MYC	chr1:169336470-169337791	K562	blood:	n/a	chr1:169336502-169336511
25	GATA2	chr1:169336395-169337949	SH-SY5Y	brain:	n/a	chr1:169336827-169336838
26	POLR2A	chr1:169336337-169338113	IMR90	lung:	n/a	n/a
27	GATA1	chr1:169336403-169337841	PBDE	blood:	n/a	chr1:169336827-169336838
28	GABPA	chr1:169336536-169337972	A549	lung:	n/a	n/a
29	PML	chr1:169336578-169338042	K562	blood:	n/a	n/a
30	RCOR1	chr1:169336589-169338077	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:169336381-169337725	H1-neurons	neurons:	n/a	n/a
32	MAZ	chr1:169336536-169338002	K562	blood:	n/a	n/a
33	POLR2A	chr1:169336471-169338041	GM12891	blood:	n/a	n/a
34	POLR2A	chr1:169336424-169336710	Hela-S3	cervix:	n/a	n/a
35	SIN3A	chr1:169336451-169338078	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr1:169336569-169337414	A549	lung:	n/a	n/a
37	MYC	chr1:169336598-169337999	NB4	blood:	n/a	n/a
38	MXI1	chr1:169336098-169338754	SK-N-SH	brain:	n/a	n/a
39	NR2F2	chr1:169336545-169338047	K562	blood:	n/a	n/a
40	GABPA	chr1:169336412-169338346	MCF-7	breast:	n/a	n/a
41	GABPA	chr1:169336568-169338194	A549	lung:	n/a	n/a
42	TEAD4	chr1:169336415-169338201	K562	blood:	n/a	n/a
43	SIN3AK20	chr1:169336381-169337921	MCF-7	breast:	n/a	n/a
44	MYC	chr1:169336590-169337932	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169075479..169078672-chr1:169335264..169338570,4	MCF-7	breast:
2	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
3	chr1:169335832..169338194-chr1:169763167..169765301,2	K562	blood:

Variant related genes	Relation type
BLZF1	TF binding region
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1014965	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10442644	0.82[ASW][hapmap];0.82[CEU][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs12116551	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs12118611	1.00[ASW][hapmap];0.82[CEU][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs12119479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12121891	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12124049	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12128350	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12140572	0.82[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12143708	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12728614	1.00[YRI][hapmap]
rs12730053	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12750775	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12758228	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17349439	0.82[ASW][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap]
rs17349579	0.84[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17577184	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1936533	0.82[YRI][hapmap]
rs2040446	0.82[ASW][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap]
rs2157597	0.82[ASW][hapmap];0.82[CEU][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap]
rs35010461	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35107735	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35220898	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs4589164	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs4656182	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4656658	0.82[ASW][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap]
rs4656664	0.82[ASW][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap]
rs4656674	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656677	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656678	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656680	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs61806989	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61807017	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6427193	0.82[ASW][hapmap];0.86[CEU][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap]
rs6656463	0.82[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap]
rs6692649	0.95[CEU][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs722145	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7368145	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7516097	0.82[YRI][hapmap]
rs7522896	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7527703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7542751	1.00[CEU][hapmap]
rs7546347	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4656671	XCL2	cis	cerebellum	SCAN
rs4656671	GPA33	cis	cerebellum	SCAN
rs4656671	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs4656671	NME7	cis	cerebellum	SCAN
rs4656671	NME7	cis	Artery Tibial	GTEx
rs4656671	CELF6	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169335600-169338200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:169335800-169336800	Flanking Active TSS	Fetal Lung	lung
3	chr1:169335800-169336800	Weak transcription	Gastric	stomach
4	chr1:169335800-169336800	Flanking Active TSS	Dnd41	blood
5	chr1:169335800-169337000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:169335800-169337800	Active TSS	Fetal Brain Female	brain
7	chr1:169335800-169338200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:169335800-169338400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:169335800-169338400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:169335800-169338400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:169335800-169338600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:169335800-169338600	Active TSS	K562	blood
13	chr1:169335800-169339000	Active TSS	NHLF	lung
14	chr1:169336000-169337800	Active TSS	Brain Angular Gyrus	brain
15	chr1:169336000-169338200	Active TSS	Colonic Mucosa	Colon
16	chr1:169336000-169338400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:169336000-169338600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr1:169336000-169339000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:169336200-169336800	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr1:169336200-169336800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:169336200-169336800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr1:169336200-169336800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr1:169336200-169336800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:169336200-169336800	Flanking Active TSS	Liver	Liver
25	chr1:169336200-169336800	Flanking Active TSS	Hela-S3	cervix
26	chr1:169336200-169336800	Flanking Active TSS	HUVEC	blood vessel
27	chr1:169336200-169336800	Flanking Active TSS	Osteobl	bone
28	chr1:169336200-169337800	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:169336200-169338200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:169336200-169338200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr1:169336200-169338200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:169336200-169338200	Active TSS	HSMM	muscle
33	chr1:169336200-169338400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:169336200-169338400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:169336200-169338400	Active TSS	A549	lung
36	chr1:169336200-169338600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:169336200-169338600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:169336200-169338600	Active TSS	Fetal Kidney	kidney
39	chr1:169336200-169339000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:169336200-169339200	Active TSS	HMEC	breast
41	chr1:169336400-169336800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr1:169336400-169336800	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr1:169336400-169336800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr1:169336400-169336800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr1:169336400-169336800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:169336400-169336800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:169336400-169336800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:169336400-169336800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr1:169336400-169336800	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr1:169336400-169336800	Flanking Active TSS	Duodenum Mucosa	Duodenum

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