Variant report

Variant	rs13013695
Chromosome Location	chr2:32391231-32391232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:315)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:315 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr2:32390238-32391251	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:32390524-32391941	GM12878	blood:	n/a	n/a
3	YY1	chr2:32390501-32391266	K562	blood:	n/a	n/a
4	POLR2A	chr2:32390270-32391813	MCF-7	breast:	n/a	n/a
5	MYBL2	chr2:32390279-32391538	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:32390279-32391296	GM12892	blood:	n/a	n/a
7	CBX3	chr2:32390170-32391291	K562	blood:	n/a	n/a
8	EGR1	chr2:32390417-32391334	HCT-116	colon:	n/a	chr2:32390858-32390871 chr2:32390859-32390869 chr2:32390855-32390869 chr2:32390895-32390909 chr2:32390857-32390871 chr2:32390854-32390863 chr2:32390859-32390870
9	SIN3AK20	chr2:32390461-32391416	SK-N-SH	brain:	n/a	n/a
10	MAX	chr2:32390481-32391298	SK-N-SH	brain:	n/a	n/a
11	CEBPD	chr2:32390407-32391447	K562	blood:	n/a	n/a
12	POLR2A	chr2:32390242-32391647	PANC-1	pancreas:	n/a	n/a
13	TAF1	chr2:32390474-32391319	PFSK-1	brain:	n/a	n/a
14	ZMIZ1	chr2:32390561-32391312	K562	blood:	n/a	n/a
15	BACH1	chr2:32390650-32391341	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr2:32390451-32391390	GM12878	blood:	n/a	n/a
17	NR2F2	chr2:32390467-32391265	MCF-7	breast:	n/a	n/a
18	NFIC	chr2:32390493-32391275	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:32390390-32391452	HUVEC	blood vessel:	n/a	n/a
20	USF2	chr2:32390528-32391274	GM12878	blood:	n/a	n/a
21	JUN	chr2:32390658-32391609	K562	blood:	n/a	n/a
22	PAX5	chr2:32390601-32391250	GM12878	blood:	n/a	chr2:32390854-32390863
23	TBL1XR1	chr2:32390512-32391660	K562	blood:	n/a	n/a
24	TAF1	chr2:32390484-32391404	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr2:32390425-32391254	GM15510	blood:	n/a	n/a
26	ELF1	chr2:32390511-32391317	HepG2	liver:	n/a	chr2:32390853-32390866
27	POLR2A	chr2:32390302-32391317	MCF-7	breast:	n/a	n/a
28	REST	chr2:32390599-32391235	K562	blood:	n/a	chr2:32390958-32390966 chr2:32391212-32391222 chr2:32390945-32390955
29	CREB1	chr2:32390369-32391388	HepG2	liver:	n/a	n/a
30	ARID3A	chr2:32390598-32391244	K562	blood:	n/a	n/a
31	ELK1	chr2:32390670-32391338	K562	blood:	n/a	n/a
32	MYBL2	chr2:32389953-32391497	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:32390221-32391903	GM12891	blood:	n/a	n/a
34	MAX	chr2:32390450-32391373	MCF-7	breast:	n/a	n/a
35	SIN3AK20	chr2:32390472-32391269	HCT-116	colon:	n/a	n/a
36	CHD2	chr2:32390197-32391584	K562	blood:	n/a	n/a
37	POLR2A	chr2:32390506-32391977	GM19099	blood:	n/a	n/a
38	SIX5	chr2:32390253-32391708	A549	lung:	n/a	n/a
39	PBX3	chr2:32390502-32391294	SK-N-SH	brain:	n/a	n/a
40	MAX	chr2:32390433-32391371	HCT-116	colon:	n/a	n/a
41	POLR2A	chr2:32390264-32391877	HepG2	liver:	n/a	n/a
42	PML	chr2:32390402-32391954	K562	blood:	n/a	n/a
43	POLR2A	chr2:32390501-32391438	Raji	blood:	n/a	n/a
44	MAX	chr2:32390593-32391245	K562	blood:	n/a	n/a
45	GTF3C2	chr2:32389913-32391268	K562	blood:	n/a	n/a
46	POLR2A	chr2:32389104-32392168	K562	blood:	n/a	n/a
47	NFATC1	chr2:32390418-32391344	GM12878	blood:	n/a	n/a
48	HEY1	chr2:32390423-32391401	HepG2	liver:	n/a	chr2:32391190-32391205
49	ATF3	chr2:32390403-32391347	A549	lung:	n/a	n/a
50	POLR2A	chr2:32390398-32391251	PANC-1	pancreas:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:32263820..32266854-chr2:32389080..32393861,5	MCF-7	breast:
2	chr2:32287339..32289467-chr2:32389793..32392170,2	MCF-7	breast:
3	chr2:32390024..32393805-chr2:32579476..32583220,6	K562	blood:
4	chr2:32263395..32265602-chr2:32389530..32391691,2	MCF-7	breast:
5	chr2:32264868..32267001-chr2:32389298..32391324,2	K562	blood:
6	chr2:32286352..32290626-chr2:32388602..32393371,12	K562	blood:
7	chr17:80055683..80056467-chr2:32390690..32391506,2	Hela-S3	cervix:
8	chr2:32389583..32392652-chr2:32503120..32506003,3	K562	blood:
9	chr2:32234641..32236375-chr2:32389314..32391737,5	MCF-7	breast:
10	chr2:32286363..32290764-chr2:32387862..32393371,13	K562	blood:
11	chr2:32287157..32290220-chr2:32389830..32392599,3	MCF-7	breast:
12	chr2:32235154..32237462-chr2:32390889..32392468,2	MCF-7	breast:
13	chr2:32233185..32238105-chr2:32388775..32395245,11	K562	blood:
14	chr2:32233077..32237611-chr2:32388376..32395245,10	K562	blood:
15	chr2:32388347..32391315-chr6:27100140..27102328,2	MCF-7	breast:
16	chr2:32389277..32392458-chr2:32500839..32506003,6	K562	blood:
17	chr2:32264101..32266985-chr2:32387828..32391332,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272716	TF binding region
ENSG00000124635	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000021574	Chromatin interaction
ENSG00000162961	Chromatin interaction
ENSG00000119820	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000115760	Chromatin interaction
ENSG00000169710	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11676456	0.82[EUR][1000 genomes]
rs11678119	0.91[MEX][hapmap]
rs11691939	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12478134	0.91[CHB][hapmap];0.84[YRI][hapmap]
rs12614686	0.91[MEX][hapmap]
rs12991444	0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap]
rs12996943	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13006495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13006880	0.90[EUR][1000 genomes]
rs17011801	0.95[CHB][hapmap];0.94[YRI][hapmap]
rs2064813	0.84[CEU][hapmap]
rs212684	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs212702	0.84[EUR][1000 genomes]
rs212736	0.88[GIH][hapmap];0.83[TSI][hapmap]
rs212742	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs212751	0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs212754	0.89[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs212761	0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2280968	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap]
rs2294178	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2366547	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs34197800	0.85[ASW][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];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs375050	0.90[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3754835	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs3769605	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs385076	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs410469	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs4530415	0.95[ASN][1000 genomes]
rs462878	0.93[GIH][hapmap];0.83[TSI][hapmap]
rs4952207	0.95[ASN][1000 genomes]
rs56322034	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6543648	0.85[AMR][1000 genomes]
rs6723154	0.91[MEX][hapmap]
rs6756085	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7562653	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs7574000	0.83[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9789593	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][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	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13013695	NLRC4	cis	lymphoblastoid	seeQTL
rs13013695	SLC30A6	cis	parietal	SCAN
rs13013695	SLC30A6	cis	cerebellum	SCAN
rs13013695	EHD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32389200-32392000	Active TSS	NHLF	lung
2	chr2:32389400-32391600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:32389400-32391800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr2:32389400-32391800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:32389400-32392000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:32389400-32392600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr2:32389400-32392600	Active TSS	K562	blood
8	chr2:32389600-32391600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:32389600-32391600	Active TSS	A549	lung
10	chr2:32389600-32391800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:32389600-32391800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:32389600-32391800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:32389600-32392200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr2:32389600-32392200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:32389600-32392200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr2:32389800-32391400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:32389800-32391400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr2:32389800-32391400	Active TSS	Fetal Kidney	kidney
19	chr2:32389800-32391400	Active TSS	HMEC	breast
20	chr2:32389800-32391600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr2:32389800-32391600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:32389800-32391600	Active TSS	Aorta	Aorta
23	chr2:32389800-32391600	Active TSS	Brain Angular Gyrus	brain
24	chr2:32389800-32391600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:32389800-32391600	Active TSS	Fetal Stomach	stomach
26	chr2:32389800-32391600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr2:32389800-32391600	Active TSS	NH-A	brain
28	chr2:32389800-32391800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:32389800-32391800	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr2:32389800-32391800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:32389800-32391800	Active TSS	Stomach Mucosa	stomach
32	chr2:32389800-32392000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:32389800-32392000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:32389800-32392000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:32389800-32392200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr2:32389800-32392200	Active TSS	H1 Cell Line	embryonic stem cell
37	chr2:32389800-32392200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:32389800-32392200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:32389800-32392200	Active TSS	Psoas Muscle	Psoas
40	chr2:32390000-32391400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:32390000-32391400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr2:32390000-32391400	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr2:32390000-32391400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr2:32390000-32391400	Active TSS	Brain Anterior Caudate	brain
45	chr2:32390000-32391400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr2:32390000-32391400	Active TSS	Fetal Brain Female	brain
47	chr2:32390000-32391400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr2:32390000-32391400	Active TSS	Fetal Lung	lung
49	chr2:32390000-32391400	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr2:32390000-32391400	Active TSS	Rectal Smooth Muscle	rectum

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