Variant report

Variant	rs12714154
Chromosome Location	chr2:86117958-86117959
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	HMGN3	chr2:86117945-86118236	K562	blood:	n/a	n/a
2	WRNIP1	chr2:86117752-86117994	GM12878	blood:	n/a	n/a
3	YY1	chr2:86117650-86118057	K562	blood:	n/a	n/a
4	TEAD4	chr2:86117951-86118358	K562	blood:	n/a	n/a
5	TEAD4	chr2:86117684-86118428	K562	blood:	n/a	n/a
6	MAFF	chr2:86117813-86118173	K562	blood:	n/a	n/a
7	GATA1	chr2:86117506-86118543	K562	blood:	n/a	chr2:86118173-86118194
8	EP300	chr2:86117911-86118354	K562	blood:	n/a	chr2:86118071-86118080
9	RCOR1	chr2:86117773-86118393	K562	blood:	n/a	n/a
10	PML	chr2:86117951-86118390	K562	blood:	n/a	n/a
11	MAX	chr2:86112960-86118329	A549	lung:	n/a	chr2:86116152-86116161 chr2:86115924-86115934
12	BHLHE40	chr2:86117909-86118217	K562	blood:	n/a	n/a
13	MYC	chr2:86117941-86118099	NB4	blood:	n/a	n/a
14	TCF12	chr2:86115901-86118059	A549	lung:	n/a	n/a
15	GATA2	chr2:86117927-86118378	K562	blood:	n/a	chr2:86118173-86118194
16	GATA2	chr2:86117853-86118336	K562	blood:	n/a	chr2:86118173-86118194
17	MAX	chr2:86117653-86118251	A549	lung:	n/a	n/a
18	CEBPD	chr2:86117935-86118439	K562	blood:	n/a	n/a
19	MAZ	chr2:86117764-86118262	K562	blood:	n/a	n/a
20	UBTF	chr2:86117799-86118135	K562	blood:	n/a	n/a
21	RCOR1	chr2:86117772-86118258	K562	blood:	n/a	n/a
22	GATA2	chr2:86117839-86118313	K562	blood:	n/a	chr2:86118173-86118194
23	MAX	chr2:86117597-86118006	K562	blood:	n/a	n/a
24	JUND	chr2:86117830-86118341	K562	blood:	n/a	chr2:86118084-86118095
25	YY1	chr2:86117629-86118014	A549	lung:	n/a	n/a
26	CCNT2	chr2:86117842-86118309	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATOH8-2	chr2:86117845-86118103	ENSG00000232504
2	lnc-ATOH8-2	chr2:86116160-86118475	NONHSAT072061
3	lnc-ATOH8-2	chr2:86117672-86118540	NONHSAT072065

Variant related genes	Relation type
ST3GAL5	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12478916	0.84[CEU][hapmap]
rs12613609	0.88[CEU][hapmap]
rs12994053	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13024999	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025142	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs13028295	0.81[JPT][hapmap]
rs13422640	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs1401383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1401385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533605	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs2010859	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2083170	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2176627	0.88[CEU][hapmap]
rs2366947	0.88[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap]
rs2366950	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2679722	0.80[TSI][hapmap]
rs28364795	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4313976	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4331504	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4553826	0.88[CEU][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap]
rs4832015	0.88[CEU][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap]
rs4832213	0.88[CEU][hapmap]
rs4832215	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4832219	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832220	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832221	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6547637	0.88[CEU][hapmap]
rs6707472	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6721125	0.88[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap]
rs6726662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6734488	0.88[CEU][hapmap]
rs6753350	0.88[CEU][hapmap]
rs7565996	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs893445	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12714154	KCMF1	cis	cerebellum	SCAN
rs12714154	PTCD3	cis	cerebellum	SCAN
rs12714154	ST3GAL5	cis	cerebellum	SCAN
rs12714154	IMMT	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86115400-86118000	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:86115600-86118000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:86116400-86118000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86116400-86118000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr2:86116600-86118000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
6	chr2:86116600-86118000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:86116600-86118000	Flanking Active TSS	Dnd41	blood
8	chr2:86116600-86118400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr2:86116800-86118000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:86116800-86118400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:86116800-86120800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:86117000-86118000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:86117000-86118000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:86117000-86118000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr2:86117000-86118000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr2:86117000-86118200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:86117000-86118200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:86117000-86118200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:86117000-86118200	Enhancers	Spleen	Spleen
20	chr2:86117000-86118400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:86117000-86118400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr2:86117000-86118400	Flanking Active TSS	A549	lung
23	chr2:86117000-86118400	Enhancers	K562	blood
24	chr2:86117200-86118000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr2:86117200-86118000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:86117200-86118000	Enhancers	Esophagus	oesophagus
27	chr2:86117200-86118000	Enhancers	NH-A	brain
28	chr2:86117200-86118200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr2:86117200-86118200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:86117200-86118200	Enhancers	Colon Smooth Muscle	Colon
31	chr2:86117200-86118200	Enhancers	HMEC	breast
32	chr2:86117200-86118400	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:86117200-86118400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr2:86117200-86118400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr2:86117200-86118600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:86117200-86120000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:86117400-86118000	Enhancers	Brain Germinal Matrix	brain
38	chr2:86117400-86118000	Enhancers	Colonic Mucosa	Colon
39	chr2:86117400-86118000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:86117400-86118000	Bivalent Enhancer	Fetal Intestine Large	intestine
41	chr2:86117400-86118000	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr2:86117400-86118000	Enhancers	Left Ventricle	heart
43	chr2:86117400-86118000	Enhancers	Lung	lung
44	chr2:86117400-86118000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
45	chr2:86117400-86118000	Enhancers	Right Ventricle	heart
46	chr2:86117400-86118000	Enhancers	Osteobl	bone
47	chr2:86117400-86118200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:86117400-86118200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:86117400-86118200	Enhancers	Primary B cells from cord blood	blood
50	chr2:86117400-86118200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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