Variant report

Variant	rs7527703
Chromosome Location	chr1:169338046-169338047
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	HCFC1	chr1:169336279-169338667	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr1:169336397-169338050	SK-N-SH	brain:	n/a	n/a
6	IRF1	chr1:169336723-169338170	K562	blood:	n/a	chr1:169337399-169337413 chr1:169337708-169337715 chr1:169337401-169337412 chr1:169337398-169337412 chr1:169337399-169337412 chr1:169337399-169337412
7	POLR2A	chr1:169337977-169338155	MCF-7	breast:	n/a	n/a
8	SMARCC1	chr1:169336736-169338109	Hela-S3	cervix:	n/a	n/a
9	TFAP2C	chr1:169336450-169338078	Hela-S3	cervix:	n/a	chr1:169337154-169337169 chr1:169337420-169337429
10	MXI1	chr1:169336053-169338642	IMR90	lung:	n/a	n/a
11	RCOR1	chr1:169336623-169338120	K562	blood:	n/a	n/a
12	POLR2A	chr1:169336337-169338113	IMR90	lung:	n/a	n/a
13	STAT3	chr1:169337734-169338170	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:169336796-169338160	GM12878	blood:	n/a	n/a
15	RCOR1	chr1:169336589-169338077	Hela-S3	cervix:	n/a	n/a
16	NFIC	chr1:169336952-169338164	GM12878	blood:	n/a	n/a
17	SIN3A	chr1:169336451-169338078	H1-hESC	embryonic stem cell:	n/a	n/a
18	MXI1	chr1:169336098-169338754	SK-N-SH	brain:	n/a	n/a
19	GABPA	chr1:169336626-169338061	SK-N-SH	brain:	n/a	n/a
20	NR2F2	chr1:169336545-169338047	K562	blood:	n/a	n/a
21	GABPA	chr1:169336412-169338346	MCF-7	breast:	n/a	n/a
22	GABPA	chr1:169336568-169338194	A549	lung:	n/a	n/a
23	TEAD4	chr1:169336415-169338201	K562	blood:	n/a	n/a
24	POLR2A	chr1:169336821-169338070	K562	blood:	n/a	n/a
25	SIN3A	chr1:169336773-169338064	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169337706..169338261-chr17:7476042..7476824,2	Hela-S3	cervix:
2	chr1:169337822..169339719-chr1:169451874..169454199,3	K562	blood:
3	chr1:169075479..169078672-chr1:169335264..169338570,4	MCF-7	breast:
4	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
5	chr1:169335832..169338194-chr1:169763167..169765301,2	K562	blood:

Variant related genes	Relation type
NME7	TF binding region
ENSG00000143153	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000161960	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];0.94[AMR][1000 genomes];0.97[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];0.81[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12121891	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12124049	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12128350	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12140572	0.82[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12143708	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12728614	1.00[YRI][hapmap]
rs12730053	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12750775	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12758228	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17349439	0.82[ASW][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap]
rs17349579	0.84[CEU][hapmap];0.88[AFR][1000 genomes];0.86[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];0.81[MEX][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap]
rs2157597	0.82[ASW][hapmap];0.82[CEU][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap]
rs35010461	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35107735	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35220898	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs4589164	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs4656182	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656658	0.82[ASW][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap]
rs4656664	0.82[ASW][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap]
rs4656671	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]
rs4656674	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656677	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656678	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656680	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61806989	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61807017	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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];0.86[EUR][1000 genomes]
rs7368145	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7516097	0.82[YRI][hapmap]
rs7522896	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7542751	1.00[CEU][hapmap]
rs7546347	0.90[AFR][1000 genomes];0.80[AMR][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
rs7527703	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs7527703	XCL2	cis	cerebellum	SCAN
rs7527703	NME7	cis	Artery Tibial	GTEx
rs7527703	NME7	cis	cerebellum	SCAN
rs7527703	GPA33	cis	cerebellum	SCAN
rs7527703	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	chr1:169335800-169338200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:169335800-169338400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:169335800-169338400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:169335800-169338400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:169335800-169338600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:169335800-169338600	Active TSS	K562	blood
8	chr1:169335800-169339000	Active TSS	NHLF	lung
9	chr1:169336000-169338200	Active TSS	Colonic Mucosa	Colon
10	chr1:169336000-169338400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:169336000-169338600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr1:169336000-169339000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:169336200-169338200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:169336200-169338200	Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:169336200-169338200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:169336200-169338200	Active TSS	HSMM	muscle
17	chr1:169336200-169338400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:169336200-169338400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:169336200-169338400	Active TSS	A549	lung
20	chr1:169336200-169338600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:169336200-169338600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:169336200-169338600	Active TSS	Fetal Kidney	kidney
23	chr1:169336200-169339000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:169336200-169339200	Active TSS	HMEC	breast
25	chr1:169336400-169338200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:169336400-169338200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:169336400-169338200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:169336400-169338200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr1:169336400-169338200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:169336400-169338200	Active TSS	Brain Anterior Caudate	brain
31	chr1:169336400-169338200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:169336400-169338200	Active TSS	Ovary	ovary
33	chr1:169336400-169338200	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:169336400-169338400	Active TSS	H1 Cell Line	embryonic stem cell
35	chr1:169336400-169338400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:169336400-169338400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr1:169336400-169338400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr1:169336400-169338400	Active TSS	Brain Germinal Matrix	brain
39	chr1:169336400-169338400	Active TSS	Fetal Intestine Small	intestine
40	chr1:169336400-169338400	Active TSS	Right Ventricle	heart
41	chr1:169336400-169338400	Active TSS	HSMMtube	muscle
42	chr1:169336400-169338400	Active TSS	NHDF-Ad	bronchial
43	chr1:169336400-169338600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:169336400-169338600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:169336400-169338600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:169336400-169338600	Active TSS	Right Atrium	heart
47	chr1:169336600-169338200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr1:169336600-169338200	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:169336600-169338200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:169336600-169338200	Active TSS	Colon Smooth Muscle	Colon

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