Variant report

Variant	rs12990400
Chromosome Location	chr2:86081014-86081015
allele	A/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	RUNX3	chr2:86079992-86081587	GM12878	blood:	n/a	chr2:86080438-86080455
2	STAT3	chr2:86080886-86081414	GM12878	blood:	n/a	chr2:86081136-86081147 chr2:86081130-86081141
3	EP300	chr2:86080876-86081544	GM12878	blood:	n/a	chr2:86081132-86081146
4	EBF1	chr2:86080080-86081484	GM12878	blood:	n/a	n/a
5	CHD1	chr2:86080048-86081222	GM12878	blood:	n/a	n/a
6	CUX1	chr2:86080757-86081546	GM12878	blood:	n/a	n/a
7	YY1	chr2:86080275-86081044	GM12878	blood:	n/a	n/a
8	RCOR1	chr2:86080014-86081631	GM12878	blood:	n/a	n/a
9	NFIC	chr2:86080204-86081622	GM12878	blood:	n/a	n/a
10	RELA	chr2:86080061-86081754	GM18951	blood:	n/a	n/a
11	EP300	chr2:86080101-86081512	GM12878	blood:	n/a	chr2:86081132-86081146
12	STAT1	chr2:86080851-86081432	GM12878	blood:	n/a	chr2:86081136-86081147 chr2:86081130-86081141
13	WRNIP1	chr2:86079960-86081035	GM12878	blood:	n/a	n/a
14	MEF2A	chr2:86080993-86081510	GM12878	blood:	n/a	chr2:86081281-86081292
15	POLR2A	chr2:86080899-86081120	HUVEC	blood vessel:	n/a	n/a
16	NFIC	chr2:86080068-86081776	GM12878	blood:	n/a	n/a
17	RELA	chr2:86080033-86081496	GM18505	blood:	n/a	n/a
18	MXI1	chr2:86080162-86081434	GM12878	blood:	n/a	n/a
19	MAX	chr2:86080023-86081431	GM12878	blood:	n/a	chr2:86080645-86080656 chr2:86080644-86080657 chr2:86080647-86080654 chr2:86080646-86080656 chr2:86080646-86080655 chr2:86080644-86080659
20	RELA	chr2:86080052-86081470	GM19099	blood:	n/a	n/a
21	TBL1XR1	chr2:86080109-86081889	GM12878	blood:	n/a	n/a
22	BATF	chr2:86080645-86081538	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:86080028-86081125	GM12878	blood:	n/a	n/a
24	IKZF1	chr2:86080188-86081462	GM12878	blood:	n/a	n/a
25	FOXM1	chr2:86079995-86081497	GM12878	blood:	n/a	n/a
26	POU2F2	chr2:86080124-86081084	GM12878	blood:	n/a	chr2:86080627-86080649
27	STAT5A	chr2:86080780-86081252	GM12878	blood:	n/a	chr2:86081136-86081147 chr2:86081130-86081141
28	BCLAF1	chr2:86080866-86081580	GM12878	blood:	n/a	chr2:86081132-86081141
29	MTA3	chr2:86079890-86081817	GM12878	blood:	n/a	n/a
30	SMC3	chr2:86080863-86081543	GM12878	blood:	n/a	n/a
31	MAZ	chr2:86080085-86081579	GM12878	blood:	n/a	chr2:86080645-86080656 chr2:86080644-86080657 chr2:86080647-86080654 chr2:86080646-86080656 chr2:86080646-86080655 chr2:86080644-86080659
32	RELA	chr2:86080209-86081494	GM19193	blood:	n/a	n/a
33	ZNF263	chr2:86080744-86081049	HEK293-T-REx	kidney:	n/a	chr2:86080893-86080902 chr2:86080879-86080900
34	BATF	chr2:86080947-86081226	GM12878	blood:	n/a	n/a
35	NFYB	chr2:86080885-86081791	GM12878	blood:	n/a	chr2:86081470-86081480 chr2:86081471-86081483
36	PAX5	chr2:86080047-86081049	GM12878	blood:	n/a	chr2:86080459-86080468
37	BCLAF1	chr2:86080049-86081286	GM12878	blood:	n/a	chr2:86081132-86081141
38	POLR2A	chr2:86080006-86081122	GM12878	blood:	n/a	n/a
39	CHD2	chr2:86079842-86081804	GM12878	blood:	n/a	n/a
40	NFATC1	chr2:86080119-86081351	GM12878	blood:	n/a	n/a
41	ATF2	chr2:86080770-86081456	GM12878	blood:	n/a	n/a
42	NFATC1	chr2:86080634-86081219	GM12878	blood:	n/a	n/a
43	BHLHE40	chr2:86080124-86081594	GM12878	blood:	n/a	n/a
44	MTA3	chr2:86080088-86081070	GM12878	blood:	n/a	n/a
45	TBP	chr2:86081014-86081704	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:86080037-86081645	GM12878	blood:	n/a	n/a
47	RELA	chr2:86080218-86081656	GM12878	blood:	n/a	n/a
48	PML	chr2:86079962-86081823	GM12878	blood:	n/a	n/a
49	RFX5	chr2:86080907-86081588	GM12878	blood:	n/a	n/a
50	FOXM1	chr2:86080129-86081688	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86074682..86077567-chr2:86080979..86083283,2	K562	blood:
2	chr2:86073388..86076182-chr2:86080776..86083283,2	K562	blood:
3	chr2:86075670..86078465-chr2:86079454..86081924,2	MCF-7	breast:

Variant related genes	Relation type
ST3GAL5	TF binding region
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10179419	0.87[CEU][hapmap]
rs10496319	0.86[CEU][hapmap]
rs10496320	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs11127003	0.92[AMR][1000 genomes]
rs11127004	0.92[AMR][1000 genomes]
rs11127006	0.92[AMR][1000 genomes]
rs11127007	0.92[AMR][1000 genomes]
rs11681961	0.87[CEU][hapmap]
rs11694145	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478916	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12614498	0.92[AMR][1000 genomes]
rs12618873	0.85[AMR][1000 genomes]
rs12622987	0.82[AMR][1000 genomes]
rs13014421	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13014890	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs13016226	0.85[AMR][1000 genomes]
rs13024123	0.83[YRI][hapmap]
rs13033743	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026675	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17026684	0.96[CEU][hapmap]
rs2280312	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2280316	0.87[CEU][hapmap]
rs3770097	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3810821	0.90[AMR][1000 genomes]
rs56049132	0.92[AMR][1000 genomes]
rs56083339	0.92[AMR][1000 genomes]
rs62147537	0.85[AMR][1000 genomes]
rs62147538	0.92[AMR][1000 genomes]
rs62147540	0.92[AMR][1000 genomes]
rs72842060	0.90[AMR][1000 genomes]
rs72842061	0.90[AMR][1000 genomes]
rs7558479	0.92[AMR][1000 genomes]
rs7572209	0.92[AMR][1000 genomes]
rs7572386	1.00[YRI][hapmap]

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86066000-86106200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:86066200-86081400	Weak transcription	Right Ventricle	heart
3	chr2:86066400-86091400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:86067000-86099000	Weak transcription	Gastric	stomach
5	chr2:86067200-86087000	Weak transcription	Fetal Brain Male	brain
6	chr2:86067400-86084800	Weak transcription	Ovary	ovary
7	chr2:86067600-86086200	Weak transcription	Fetal Brain Female	brain
8	chr2:86071800-86096200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:86072000-86090400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:86072000-86096800	Weak transcription	Psoas Muscle	Psoas
11	chr2:86073000-86083600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:86074000-86089800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:86074600-86089600	Weak transcription	NH-A	brain
14	chr2:86074800-86086200	Weak transcription	HSMM	muscle
15	chr2:86075200-86082400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:86075400-86114000	Weak transcription	Aorta	Aorta
17	chr2:86076000-86090400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:86076800-86081400	Weak transcription	Right Atrium	heart
19	chr2:86077200-86088600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:86077600-86082400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:86078400-86081600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:86078400-86081800	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:86078400-86082000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:86078400-86082000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr2:86078600-86081600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr2:86078600-86081600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:86078600-86081800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr2:86079000-86092000	Weak transcription	Esophagus	oesophagus
29	chr2:86079200-86082200	Enhancers	Placenta	Placenta
30	chr2:86079200-86090400	Strong transcription	A549	lung
31	chr2:86079200-86092000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:86079200-86092600	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:86079200-86092800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:86079400-86081600	Active TSS	Rectal Smooth Muscle	rectum
35	chr2:86079400-86082000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr2:86079400-86083200	Weak transcription	HMEC	breast
37	chr2:86079600-86081800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:86079600-86082200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr2:86079600-86087800	Weak transcription	Osteobl	bone
40	chr2:86079600-86106200	Weak transcription	Brain Germinal Matrix	brain
41	chr2:86079800-86081600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:86079800-86081600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr2:86079800-86081600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:86079800-86081600	Genic enhancers	Fetal Muscle Leg	muscle
45	chr2:86079800-86081800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr2:86079800-86082000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr2:86080000-86081400	Enhancers	Brain Anterior Caudate	brain
48	chr2:86080000-86081600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr2:86080000-86081600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:86080000-86081600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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