Variant report

Variant	rs12702466
Chromosome Location	chr7:6048359-6048360
allele	C/T
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	SP4	chr7:6048273-6049317	H1-hESC	embryonic stem cell:	n/a	n/a
2	BHLHE40	chr7:6048295-6049309	K562	blood:	n/a	n/a
3	YY1	chr7:6048298-6049149	SK-N-SH	brain:	n/a	chr7:6048528-6048547
4	POLR2A	chr7:6047651-6049344	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:6048355-6049238	GM12878	blood:	n/a	n/a
6	MAX	chr7:6048321-6049321	HepG2	liver:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
7	POU2F2	chr7:6047775-6049268	GM12878	blood:	n/a	chr7:6048036-6048044 chr7:6048036-6048046 chr7:6048033-6048048 chr7:6048036-6048045 chr7:6048035-6048047 chr7:6048035-6048045 chr7:6048036-6048046 chr7:6048037-6048044 chr7:6048033-6048047
8	MAX	chr7:6048270-6049352	MCF-7	breast:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
9	BCL3	chr7:6048341-6049310	A549	lung:	n/a	chr7:6049244-6049257
10	E2F6	chr7:6048333-6049269	Hela-S3	cervix:	n/a	chr7:6049157-6049166 chr7:6048585-6048600 chr7:6048580-6048594 chr7:6049050-6049061 chr7:6048832-6048841 chr7:6048850-6048859
11	POLR2A	chr7:6048262-6048793	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr7:6048354-6049370	K562	blood:	n/a	n/a
13	MXI1	chr7:6047704-6049576	SK-N-SH	brain:	n/a	n/a
14	MYC	chr7:6048252-6049365	K562	blood:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
15	MYC	chr7:6048278-6049340	Hela-S3	cervix:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
16	PML	chr7:6048311-6049315	MCF-7	breast:	n/a	n/a
17	HEY1	chr7:6048274-6049433	HepG2	liver:	n/a	chr7:6048832-6048841
18	MAX	chr7:6048258-6049431	K562	blood:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
19	TEAD4	chr7:6048298-6049334	SK-N-SH	brain:	n/a	n/a
20	ELF1	chr7:6048319-6049345	MCF-7	breast:	n/a	n/a
21	YY1	chr7:6048352-6048850	H1-hESC	embryonic stem cell:	n/a	chr7:6048528-6048547
22	CTCF	chr7:6048340-6048490	GM12869	blood:	n/a	n/a
23	MAX	chr7:6048293-6049476	HCT-116	colon:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
24	RUNX3	chr7:6048286-6049157	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:6048257-6049487	PANC-1	pancreas:	n/a	n/a
26	MBD4	chr7:6048322-6049290	HepG2	liver:	n/a	n/a
27	POLR2A	chr7:6048280-6049348	ECC-1	luminal epithelium:	n/a	n/a
28	MAX	chr7:6048289-6049478	HepG2	liver:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
29	POLR2A	chr7:6047744-6049224	GM12892	blood:	n/a	n/a
30	POLR2A	chr7:6048246-6049243	GM12891	blood:	n/a	n/a
31	POLR2A	chr7:6048302-6049333	HL-60	blood:	n/a	n/a
32	FOXP2	chr7:6048333-6049253	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr7:6048320-6049352	HCT-116	colon:	n/a	n/a
34	POLR2A	chr7:6048337-6049331	H1-neurons	neurons:	n/a	n/a
35	MYC	chr7:6048334-6049433	K562	blood:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
36	HEY1	chr7:6048243-6049359	K562	blood:	n/a	chr7:6048832-6048841
37	MYC	chr7:6048302-6049384	NB4	blood:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
38	CTCF	chr7:6048320-6048470	MCF-7	breast:	n/a	n/a
39	HDAC2	chr7:6048323-6048534	K562	blood:	n/a	n/a
40	SIN3AK20	chr7:6048353-6049286	K562	blood:	n/a	n/a
41	POLR2A	chr7:6048261-6049280	A549	lung:	n/a	n/a
42	E2F6	chr7:6048319-6049323	A549	lung:	n/a	chr7:6049157-6049166 chr7:6048585-6048600 chr7:6048580-6048594 chr7:6049050-6049061 chr7:6048832-6048841 chr7:6048850-6048859
43	REST	chr7:6048237-6049307	SK-N-SH	brain:	n/a	chr7:6049175-6049188 chr7:6049178-6049191
44	TFAP2C	chr7:6048283-6049260	Hela-S3	cervix:	n/a	chr7:6048686-6048701
45	MYBL2	chr7:6048233-6049346	HepG2	liver:	n/a	n/a
46	MAX	chr7:6048237-6049365	ECC-1	luminal epithelium:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
47	TBL1XR1	chr7:6048327-6049245	K562	blood:	n/a	n/a
48	MAX	chr7:6048349-6049312	ECC-1	luminal epithelium:	n/a	chr7:6048520-6048529 chr7:6049145-6049155
49	CREB1	chr7:6048263-6049334	GM12878	blood:	n/a	n/a
50	IRF4	chr7:6048252-6048927	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6047579..6050679-chr7:6097211..6100186,3	MCF-7	breast:
2	chr7:6047363..6049354-chr7:6063912..6067391,3	MCF-7	breast:
3	chr7:6041705..6045263-chr7:6045824..6048661,5	MCF-7	breast:
4	chr7:6046967..6050535-chr7:6141219..6149580,10	K562	blood:
5	chr12:120729471..120730015-chr7:6048155..6048715,2	NB4	blood:
6	chr7:6047930..6051239-chr7:6095534..6098918,6	K562	blood:
7	chr1:153598961..153599821-chr7:6048148..6049140,2	Hela-S3	cervix:
8	chr7:6046629..6049121-chr7:6054916..6059212,5	K562	blood:
9	chr7:6047026..6051403-chr7:6141746..6146462,7	K562	blood:
10	chr7:6047262..6048916-chr7:6096593..6098744,2	MCF-7	breast:
11	chr17:39845083..39845933-chr7:6048217..6048963,2	NB4	blood:
12	chr7:6047404..6049912-chr7:6142714..6146343,4	MCF-7	breast:
13	chr7:6047922..6050389-chr7:6388573..6391369,3	K562	blood:
14	chr7:6046534..6048837-chr7:6387102..6390061,2	MCF-7	breast:
15	chr7:6047355..6050049-chr7:6209625..6211423,2	MCF-7	breast:
16	chr7:6044783..6046787-chr7:6047336..6049227,2	K562	blood:

Variant related genes	Relation type
PMS2	TF binding region
ENSG00000201990	TF binding region
AIMP2	TF binding region
ENSG00000201990	Chromatin interaction
ENSG00000207217	Chromatin interaction
ENSG00000178397	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000106346	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000008256	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1062372	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702467	0.95[ASN][1000 genomes]
rs2302335	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34097030	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3735295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779108	0.96[ASN][1000 genomes]
rs6945922	0.97[ASN][1000 genomes]
rs6978310	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6979676	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7797466	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7803118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7811735	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
2	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
3	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
5	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
8	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
10	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
11	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
12	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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	127 gene(s)	inside rSNPs	diseases
13	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
14	nsv830894	chr7:5889658-6072215	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
16	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
17	nsv605998	chr7:6035065-6102034	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1018388	chr7:6038713-6131169	Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
19	nsv970441	chr7:6039097-6048842	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12702466	PMS2	cis	Thyroid	GTEx
rs12702466	PMS2	cis	Artery Tibial	GTEx
rs12702466	EIF2AK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6047000-6049800	Active TSS	A549	lung
2	chr7:6047000-6050000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:6047000-6050200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:6047000-6050200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr7:6047200-6050200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:6047400-6049600	Active TSS	Fetal Kidney	kidney
7	chr7:6047400-6049800	Active TSS	K562	blood
8	chr7:6047600-6048600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:6047600-6048600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:6047600-6049600	Active TSS	Rectal Smooth Muscle	rectum
11	chr7:6047600-6049800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:6047600-6049800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:6047600-6049800	Active TSS	Fetal Brain Female	brain
14	chr7:6047600-6049800	Active TSS	Hela-S3	cervix
15	chr7:6047600-6049800	Active TSS	HMEC	breast
16	chr7:6047600-6049800	Active TSS	HSMM	muscle
17	chr7:6047600-6050000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:6047600-6050000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr7:6047600-6050000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr7:6047600-6050000	Active TSS	HSMMtube	muscle
21	chr7:6047600-6050200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr7:6047600-6050200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:6047600-6050400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:6047800-6048400	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr7:6047800-6048400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr7:6047800-6049000	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr7:6047800-6049800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:6047800-6049800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:6047800-6049800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr7:6047800-6049800	Active TSS	Muscle Satellite Cultured Cells	--
31	chr7:6047800-6049800	Active TSS	NH-A	brain
32	chr7:6047800-6049800	Active TSS	NHEK	skin
33	chr7:6047800-6050000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:6047800-6050000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr7:6047800-6050000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:6047800-6050200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr7:6047800-6050200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr7:6047800-6050200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:6047800-6050200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr7:6047800-6050400	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr7:6047800-6050400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:6047800-6050400	Active TSS	GM12878-XiMat	blood
43	chr7:6048000-6048400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr7:6048000-6048400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr7:6048000-6048400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:6048000-6048400	Active TSS	Right Atrium	heart
47	chr7:6048000-6048600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr7:6048000-6048600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr7:6048000-6048600	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr7:6048000-6048600	Bivalent/Poised TSS	HepG2	liver

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