Variant report

Variant	rs12991444
Chromosome Location	chr2:32265125-32265126
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:405)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:405 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr2:32264698-32265495	GM12878	blood:	n/a	n/a
2	TBP	chr2:32264551-32265396	K562	blood:	n/a	n/a
3	TAF1	chr2:32264666-32265199	SK-N-SH	brain:	n/a	n/a
4	YY1	chr2:32264357-32265293	HepG2	liver:	n/a	chr2:32264628-32264639
5	REST	chr2:32264649-32265220	A549	lung:	n/a	chr2:32264671-32264689 chr2:32265110-32265130
6	POLR2A	chr2:32264547-32265363	NB4	blood:	n/a	n/a
7	BHLHE40	chr2:32264231-32265179	K562	blood:	n/a	chr2:32264633-32264649
8	MYC	chr2:32264573-32265185	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr2:32264525-32265262	SK-N-SH	brain:	n/a	n/a
10	BCL3	chr2:32264534-32265325	A549	lung:	n/a	n/a
11	POLR2A	chr2:32264479-32265267	H1-neurons	neurons:	n/a	n/a
12	NRF1	chr2:32264719-32265225	K562	blood:	n/a	chr2:32264896-32264910 chr2:32264899-32264913 chr2:32264899-32264910 chr2:32264899-32264910 chr2:32264901-32264910
13	POLR2A	chr2:32264503-32265228	GM12878	blood:	n/a	n/a
14	CTCF	chr2:32265020-32265170	WERI-Rb-1	eye:	n/a	n/a
15	TAF1	chr2:32264656-32265243	GM12892	blood:	n/a	n/a
16	MAX	chr2:32264648-32265146	HepG2	liver:	n/a	n/a
17	ZKSCAN1	chr2:32264668-32265136	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr2:32264199-32265133	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr2:32264972-32265137	MCF-7	breast:	n/a	n/a
20	SPI1	chr2:32264769-32265468	HL-60	blood:	n/a	chr2:32265166-32265179
21	MYC	chr2:32264655-32265263	K562	blood:	n/a	n/a
22	ATF3	chr2:32264602-32265202	GM12878	blood:	n/a	n/a
23	TAF1	chr2:32264693-32265179	GM12892	blood:	n/a	n/a
24	POLR2A	chr2:32264423-32265216	A549	lung:	n/a	n/a
25	POLR2A	chr2:32264640-32265267	HCT-116	colon:	n/a	n/a
26	ELF1	chr2:32264697-32265355	A549	lung:	n/a	n/a
27	TAF1	chr2:32264700-32265266	GM12891	blood:	n/a	n/a
28	CREB1	chr2:32264279-32265381	HepG2	liver:	n/a	n/a
29	REST	chr2:32264904-32265137	H1-hESC	embryonic stem cell:	n/a	chr2:32265110-32265130
30	TAF7	chr2:32264639-32265258	H1-hESC	embryonic stem cell:	n/a	n/a
31	TEAD4	chr2:32264542-32265492	K562	blood:	n/a	n/a
32	NRF1	chr2:32264699-32265354	GM12878	blood:	n/a	chr2:32264896-32264910 chr2:32264899-32264913 chr2:32264899-32264910 chr2:32264899-32264910 chr2:32264901-32264910
33	POLR2A	chr2:32264622-32265159	HepG2	liver:	n/a	n/a
34	YY1	chr2:32264763-32265296	K562	blood:	n/a	n/a
35	TAF1	chr2:32264689-32265241	GM12891	blood:	n/a	n/a
36	FOSL2	chr2:32264600-32265291	A549	lung:	n/a	n/a
37	MAX	chr2:32264492-32265334	MCF-7	breast:	n/a	n/a
38	GTF2F1	chr2:32264126-32265301	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr2:32264638-32265228	HUVEC	blood vessel:	n/a	n/a
40	ZMIZ1	chr2:32264720-32265262	K562	blood:	n/a	n/a
41	ZNF384	chr2:32264705-32265346	K562	blood:	n/a	n/a
42	CTCF	chr2:32264920-32265170	GM12864	blood:	n/a	n/a
43	YY1	chr2:32264301-32265246	SK-N-SH_RA	brain:	n/a	chr2:32264628-32264639
44	POLR2A	chr2:32264549-32265286	A549	lung:	n/a	n/a
45	RCOR1	chr2:32264700-32265179	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:32264610-32265345	K562	blood:	n/a	n/a
47	POLR2A	chr2:32264637-32265445	HL-60	blood:	n/a	n/a
48	TAF1	chr2:32264426-32265314	K562	blood:	n/a	n/a
49	TAF1	chr2:32264674-32265179	GM12878	blood:	n/a	n/a
50	ETS1	chr2:32264473-32265218	K562	blood:	n/a	chr2:32265168-32265175

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:32265121-32265171	BJ	skin:	n/a
2	chr2:32265121-32265171	GM12892	blood:	n/a
3	chr2:32265121-32265171	Jurkat	blood:	n/a
4	chr2:32265121-32265171	LNCaP	prostate:	n/a
5	chr2:32265121-32265171	GM19239	blood:	n/a
6	chr2:32265121-32265171	HL-60	blood:	n/a
7	chr2:32265121-32265171	AG09309	skin:	n/a
8	chr2:32265121-32265171	MCF10A-Er-Src	breast:	n/a
9	chr2:32265121-32265171	HCM	heart:	n/a
10	chr2:32265121-32265171	Hela-S3	cervix:	n/a
11	chr2:32265121-32265171	HAEpiC	amniotic membrane:	n/a
12	chr2:32265121-32265171	SKMC	muscle:	n/a
13	chr2:32265121-32265171	HEK293	kidney:	embryo
14	chr2:32265121-32265171	AG09319	gingival:	n/a
15	chr2:32265121-32265171	AoSMC	blood vessel:	n/a
16	chr2:32265121-32265171	GM12891	blood:	n/a
17	chr2:32265121-32265171	AG10803	skin:	n/a
18	chr2:32265121-32265171	NHBE	bronchial:	n/a
19	chr2:32265121-32265171	NHDF-neo	bronchial:	n/a
20	chr2:32265121-32265171	HEEpiC	esophagus:	n/a
21	chr2:32265121-32265171	HCPEpiC	choroid plexus:	n/a
22	chr2:32265121-32265171	HRPEpiC	eye:	n/a
23	chr2:32265121-32265171	BE2_C	brain:	n/a
24	chr2:32265121-32265171	K562	blood:	n/a
25	chr2:32265121-32265171	Caco-2	colon:	n/a
26	chr2:32265121-32265171	RPTEC	kidney:	n/a
27	chr2:32265121-32265171	AG04449	skin:	fetal
28	chr2:32265121-32265171	HMEC	breast:	n/a
29	chr2:32265121-32265171	AG04450	lung:	fetal
30	chr2:32265121-32265171	SAEC	small airway:	n/a
31	chr2:32265121-32265171	SK-N-SH_RA	brain:	n/a
32	chr2:32265121-32265171	HRE	kidney:	n/a
33	chr2:32265121-32265171	IMR90	lung:	fetal
34	chr2:32265121-32265171	U87	brain:	n/a
35	chr2:32265121-32265171	SK-N-SH	brain:	n/a
36	chr2:32265121-32265171	HIPEpiC	eye:	n/a
37	chr2:32265121-32265171	PrEC	prostate:	n/a
38	chr2:32265121-32265171	ovcar-3	ovarian:	n/a
39	chr2:32265121-32265171	HCT-116	colon:	n/a
40	chr2:32265121-32265171	ProgFib	skin:	n/a
41	chr2:32265121-32265171	T-47D	breast:	n/a
42	chr2:32265121-32265171	H1-hESC	embryonic stem cell:	embryo
43	chr2:32265121-32265171	HepG2	liver:	n/a
44	chr2:32265121-32265171	NB4	blood:	n/a
45	chr2:32265121-32265171	Hepatocyte	liver:	n/a
46	chr2:32265121-32265171	HCF	heart:	n/a
47	chr2:32265121-32265171	PFSK-1	brain:	n/a
48	chr2:32265121-32265171	HPAEpiC	pulmonary alveolar:	n/a
49	chr2:32265121-32265171	CMK	blood:	n/a
50	chr2:32265121-32265171	GM12878	blood:	n/a

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:32264101..32266985-chr2:32387828..32391332,6	K562	blood:
2	chr2:32233869..32239615-chr2:32259766..32267170,13	K562	blood:
3	chr2:32264410..32265258-chr2:58467951..58468569,2	HCT-116	colon:
4	chr2:32263820..32266854-chr2:32389080..32393861,5	MCF-7	breast:
5	chr2:32256593..32258983-chr2:32264905..32266579,2	K562	blood:
6	chr2:32234151..32237531-chr2:32262421..32266825,7	K562	blood:
7	chr2:32233050..32238839-chr2:32262715..32266551,10	MCF-7	breast:
8	chr2:32262396..32266546-chr2:32286416..32291415,12	K562	blood:
9	chr2:32263267..32267327-chr2:32283931..32290396,13	MCF-7	breast:
10	chr2:32231133..32238127-chr2:32263164..32266706,7	MCF-7	breast:
11	chr15:65596727..65597260-chr2:32264848..32265472,2	NB4	blood:
12	chr2:32263531..32265848-chr2:32287148..32290470,4	K562	blood:
13	chr2:32264894..32267187-chr2:32274162..32276934,2	MCF-7	breast:
14	chr2:32263395..32265602-chr2:32389530..32391691,2	MCF-7	breast:
15	chr2:32264484..32265161-chr20:34638470..34639034,2	NB4	blood:
16	chr2:32262818..32267061-chr2:32286978..32290820,6	MCF-7	breast:
17	chr2:32264868..32267001-chr2:32389298..32391324,2	K562	blood:
18	chr2:32264450..32265171-chr2:32390311..32391216,2	MCF-7	breast:

No data

Variant related genes	Relation type
DPY30	TF binding region
DPY30	CpG island
ENSG00000152683	Chromatin interaction
ENSG00000260032	Chromatin interaction
ENSG00000271228	Chromatin interaction
ENSG00000021574	Chromatin interaction
ENSG00000273063	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000115392	Chromatin interaction
ENSG00000272716	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11124272	0.86[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs11678119	0.86[MEX][hapmap]
rs11691939	0.86[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs12468012	0.81[EUR][1000 genomes]
rs12478134	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12614686	0.87[MEX][hapmap]
rs13006495	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap]
rs13013695	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]
rs17011801	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs177082	0.87[CEU][hapmap]
rs212689	0.87[CEU][hapmap]
rs212751	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs212754	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs212761	0.86[CEU][hapmap];0.84[JPT][hapmap]
rs2280968	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2366547	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34197800	0.86[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs35196278	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs375050	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs3754835	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs3769605	0.86[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs3769611	0.84[CHD][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs462878	0.87[CEU][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap]
rs4952203	0.82[GIH][hapmap]
rs61399065	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6723154	0.86[MEX][hapmap]
rs71446036	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7556942	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7574000	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12991444	NLRC4	cis	lymphoblastoid	seeQTL
rs12991444	SLC30A6	cis	cerebellum	SCAN
rs12991444	SLC30A6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32263600-32265400	Active TSS	Fetal Intestine Large	intestine
2	chr2:32263600-32265600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:32263600-32265600	Active TSS	Fetal Brain Female	brain
4	chr2:32263800-32265200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:32263800-32265200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:32263800-32265200	Active TSS	NHLF	lung
7	chr2:32263800-32265200	Active TSS	Osteobl	bone
8	chr2:32263800-32265400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr2:32263800-32265400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:32263800-32265400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:32263800-32265400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:32263800-32265400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:32263800-32265400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr2:32263800-32265400	Active TSS	Brain Germinal Matrix	brain
15	chr2:32263800-32265400	Active TSS	HSMM	muscle
16	chr2:32263800-32265400	Active TSS	NH-A	brain
17	chr2:32263800-32265600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr2:32263800-32265600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:32263800-32265600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr2:32263800-32265600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr2:32263800-32265600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr2:32263800-32265600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:32263800-32265600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:32263800-32265800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:32264000-32265200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:32264000-32265200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:32264000-32265400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:32264000-32265400	Active TSS	Colonic Mucosa	Colon
29	chr2:32264000-32265400	Active TSS	Pancreas	Pancrea
30	chr2:32264000-32265400	Active TSS	Psoas Muscle	Psoas
31	chr2:32264000-32265400	Active TSS	NHDF-Ad	bronchial
32	chr2:32264000-32265600	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr2:32264000-32265600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:32264000-32265600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:32264000-32265600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr2:32264000-32265600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:32264000-32265600	Active TSS	Brain Substantia Nigra	brain
38	chr2:32264200-32265200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:32264200-32265200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:32264200-32265200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:32264200-32265200	Active TSS	Esophagus	oesophagus
42	chr2:32264200-32265200	Active TSS	Fetal Intestine Small	intestine
43	chr2:32264200-32265200	Active TSS	Gastric	stomach
44	chr2:32264200-32265200	Active TSS	Lung	lung
45	chr2:32264200-32265200	Active TSS	Placenta Amnion	Placenta Amnion
46	chr2:32264200-32265200	Active TSS	A549	lung
47	chr2:32264200-32265400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr2:32264200-32265400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:32264200-32265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:32264200-32265400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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