Variant report

Variant	rs1527423
Chromosome Location	chr7:99691740-99691741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:110 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99688274-99694487	K562	blood:	n/a	n/a
2	POLR2A	chr7:99688737-99692171	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:99690378-99692039	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr7:99688464-99692163	HL-60	blood:	n/a	n/a
5	POLR2A	chr7:99690593-99692003	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:99687882-99694248	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr7:99688195-99692477	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:99688125-99694156	A549	lung:	n/a	n/a
9	ATF2	chr7:99691707-99692207	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr7:99688146-99692390	GM12892	blood:	n/a	n/a
11	POLR2A	chr7:99691184-99692069	GM12891	blood:	n/a	n/a
12	POLR2A	chr7:99688045-99692643	U87	brain:	n/a	n/a
13	HEY1	chr7:99688532-99692174	K562	blood:	n/a	n/a
14	POLR2A	chr7:99687987-99692292	GM12891	blood:	n/a	n/a
15	POLR2A	chr7:99688636-99692204	K562	blood:	n/a	n/a
16	POLR2A	chr7:99688437-99692535	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr7:99691126-99692067	GM12892	blood:	n/a	n/a
18	MAFK	chr7:99691270-99691866	HepG2	liver:	n/a	chr7:99691670-99691685
19	POLR2A	chr7:99690393-99692048	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:99690615-99692551	U87	brain:	n/a	n/a
21	PBX3	chr7:99690820-99692038	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr7:99691667-99692093	MCF10A-Er-Src	breast:	n/a	n/a
23	MAFK	chr7:99691322-99691879	K562	blood:	n/a	chr7:99691670-99691685
24	POLR2A	chr7:99687998-99697728	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr7:99688270-99692495	GM12891	blood:	n/a	n/a
26	POLR2A	chr7:99690558-99692057	GM18951	blood:	n/a	n/a
27	PML	chr7:99688566-99692628	K562	blood:	n/a	n/a
28	MAFK	chr7:99691259-99691957	H1-hESC	embryonic stem cell:	n/a	chr7:99691670-99691685
29	MAFF	chr7:99691352-99691883	K562	blood:	n/a	chr7:99691669-99691687
30	POLR2A	chr7:99688018-99692650	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr7:99688020-99692610	U87	brain:	n/a	n/a
32	POLR2A	chr7:99688044-99692355	GM12892	blood:	n/a	n/a
33	POLR2A	chr7:99688357-99692123	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr7:99687915-99694390	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr7:99688235-99694055	K562	blood:	n/a	n/a
36	POLR2A	chr7:99688771-99692413	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr7:99687562-99696983	HepG2	liver:	n/a	n/a
38	POLR2A	chr7:99688522-99694500	K562	blood:	n/a	n/a
39	POLR2A	chr7:99688060-99692203	GM12892	blood:	n/a	n/a
40	POLR2A	chr7:99688533-99692164	GM12891	blood:	n/a	n/a
41	ZMIZ1	chr7:99691596-99691786	K562	blood:	n/a	n/a
42	POLR2A	chr7:99691551-99692059	PBDE	blood:	n/a	n/a
43	POLR2A	chr7:99687926-99694337	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr7:99691362-99692447	K562	blood:	n/a	n/a
45	POLR2A	chr7:99688553-99692466	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr7:99690340-99692132	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAFK	chr7:99691363-99691863	Hela-S3	cervix:	n/a	chr7:99691670-99691685
48	POLR2A	chr7:99690426-99692048	A549	lung:	n/a	n/a
49	POLR2A	chr7:99690501-99692007	GM18505	blood:	n/a	n/a
50	POLR2A	chr7:99690519-99692551	U87	brain:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:99691720-99691770	BE2_C	brain:	n/a
2	chr7:99691720-99691770	PFSK-1	brain:	n/a
3	chr7:99691734-99691784	SK-N-MC	brain:	n/a
4	chr7:99691720-99691770	Hela-S3	cervix:	n/a
5	chr7:99691720-99691770	T-47D	breast:	n/a
6	chr7:99691720-99691770	MCF-7	breast:	n/a
7	chr7:99691734-99691784	HRPEpiC	eye:	n/a
8	chr7:99691720-99691770	HEEpiC	esophagus:	n/a
9	chr7:99691734-99691784	NB4	blood:	n/a
10	chr7:99691734-99691784	HPAEpiC	pulmonary alveolar:	n/a
11	chr7:99691720-99691770	HMEC	breast:	n/a
12	chr7:99691720-99691770	A549	lung:	n/a
13	chr7:99691734-99691784	PFSK-1	brain:	n/a
14	chr7:99691720-99691770	GM19239	blood:	n/a
15	chr7:99691734-99691784	HepG2	liver:	n/a
16	chr7:99691720-99691770	BJ	skin:	n/a
17	chr7:99691720-99691770	AG09319	gingival:	n/a
18	chr7:99691720-99691770	U87	brain:	n/a
19	chr7:99691734-99691784	LNCaP	prostate:	n/a
20	chr7:99691734-99691784	HCM	heart:	n/a
21	chr7:99691720-99691770	ovcar-3	ovarian:	n/a
22	chr7:99691720-99691770	NH-A	brain:	n/a
23	chr7:99691720-99691770	NHDF-neo	bronchial:	n/a
24	chr7:99691734-99691784	Hepatocyte	liver:	n/a
25	chr7:99691720-99691770	RPTEC	kidney:	n/a
26	chr7:99691720-99691770	CMK	blood:	n/a
27	chr7:99691720-99691770	HPAEpiC	pulmonary alveolar:	n/a
28	chr7:99691734-99691784	HAEpiC	amniotic membrane:	n/a
29	chr7:99691734-99691784	MCF-7	breast:	n/a
30	chr7:99691734-99691784	HIPEpiC	eye:	n/a
31	chr7:99691720-99691770	SK-N-MC	brain:	n/a
32	chr7:99691734-99691784	GM12892	blood:	n/a
33	chr7:99691734-99691784	AG04449	skin:	fetal
34	chr7:99691720-99691770	SKMC	muscle:	n/a
35	chr7:99691720-99691770	AG04450	lung:	fetal
36	chr7:99691734-99691784	RPTEC	kidney:	n/a
37	chr7:99691734-99691784	AG04450	lung:	fetal
38	chr7:99691720-99691770	AG09309	skin:	n/a
39	chr7:99691720-99691770	LNCaP	prostate:	n/a
40	chr7:99691734-99691784	BE2_C	brain:	n/a
41	chr7:99691720-99691770	AoSMC	blood vessel:	n/a
42	chr7:99691734-99691784	SAEC	small airway:	n/a
43	chr7:99691734-99691784	GM19239	blood:	n/a
44	chr7:99691720-99691770	K562	blood:	n/a
45	chr7:99691720-99691770	HEK293	kidney:	embryo
46	chr7:99691734-99691784	SKMC	muscle:	n/a
47	chr7:99691720-99691770	GM12892	blood:	n/a
48	chr7:99691734-99691784	GM12891	blood:	n/a
49	chr7:99691720-99691770	NHBE	bronchial:	n/a
50	chr7:99691734-99691784	NHBE	bronchial:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99690528..99692803-chr7:99751485..99754515,3	MCF-7	breast:
2	chr17:61776660..61777476-chr7:99691264..99692181,2	NB4	blood:

No data

Variant related genes	Relation type
MIR25	TF binding region
MIR106B	TF binding region
MIR93	TF binding region
MIR106B	CpG island
MIR25	CpG island
MIR93	CpG island
ENSG00000136490	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000266154	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10231604	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs10281368	0.95[YRI][hapmap]
rs11764584	0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs11771139	0.91[YRI][hapmap]
rs13223792	0.82[YRI][hapmap]
rs1880949	0.91[YRI][hapmap]
rs1918353	0.89[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs2272337	0.84[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs2272338	0.87[MEX][hapmap]
rs2293479	0.82[YRI][hapmap]
rs2405440	0.89[CEU][hapmap]
rs35146811	0.91[YRI][hapmap]
rs3736590	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs3800951	0.89[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs3823646	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs4134903	0.91[YRI][hapmap]
rs4134917	0.88[GIH][hapmap];0.87[MEX][hapmap]
rs4729567	0.87[MEX][hapmap]
rs4729568	0.87[MEX][hapmap]
rs4729577	0.87[MEX][hapmap]
rs6960432	0.87[MEX][hapmap]
rs7785392	0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs7807156	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7807641	0.89[CEU][hapmap]
rs9649220	0.87[MEX][hapmap]
rs999885	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1527423	ZSCAN21	cis	parietal	SCAN
rs1527423	AP4M1	cis	Artery Tibial	GTEx
rs1527423	GATS	cis	parietal	SCAN
rs1527423	AP4M1	cis	lymphoblastoid	seeQTL
rs1527423	AP4M1	cis	cerebellum	SCAN
rs1527423	ZKSCAN1	cis	multi-tissue	Pritchard
rs1527423	AP4M1	cis	Thyroid	GTEx
rs1527423	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs1527423	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs1527423	TAF6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99687200-99693000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99687400-99697200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:99687600-99696000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr7:99687600-99696600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:99687600-99696800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:99687800-99691800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:99687800-99692000	Genic enhancers	NH-A	brain
8	chr7:99687800-99696000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:99687800-99696600	Strong transcription	Fetal Intestine Small	intestine
10	chr7:99688000-99693000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:99688000-99695400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:99688000-99695600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:99688000-99695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:99688000-99696000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:99688000-99696200	Strong transcription	Fetal Intestine Large	intestine
16	chr7:99688000-99696400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:99688000-99696400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:99688000-99696400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:99688000-99696400	Strong transcription	Thymus	Thymus
20	chr7:99688000-99696600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr7:99688000-99696600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:99688000-99696600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr7:99688000-99696600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr7:99688000-99696600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr7:99688000-99696800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:99688000-99696800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr7:99688000-99696800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:99688000-99696800	Strong transcription	Brain Angular Gyrus	brain
29	chr7:99688000-99697000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:99688000-99697000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:99688000-99697000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:99688000-99697000	Strong transcription	A549	lung
33	chr7:99688000-99697000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr7:99688000-99697200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:99688000-99697200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr7:99688000-99697200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:99688000-99697200	Strong transcription	Brain Anterior Caudate	brain
38	chr7:99688000-99697200	Strong transcription	Brain Hippocampus Middle	brain
39	chr7:99688000-99697200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:99688000-99697200	Strong transcription	Left Ventricle	heart
41	chr7:99688000-99697200	Strong transcription	Ovary	ovary
42	chr7:99688000-99697200	Strong transcription	NHEK	skin
43	chr7:99688200-99695200	Strong transcription	Fetal Lung	lung
44	chr7:99688200-99695400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:99688200-99695800	Strong transcription	Primary T cells from cord blood	blood
46	chr7:99688200-99696200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:99688200-99696200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:99688200-99696400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:99688200-99696600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr7:99688200-99696600	Strong transcription	H9 Cell Line	embryonic stem cell

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