Variant report

Variant	rs2278089
Chromosome Location	chr2:152146672-152146673
allele	A/C
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	TBL1XR1	chr2:152145812-152146767	GM12878	blood:	n/a	n/a
2	JUND	chr2:152145780-152146846	K562	blood:	n/a	chr2:152146649-152146659 chr2:152146649-152146659
3	MAFK	chr2:152146253-152146951	Hela-S3	cervix:	n/a	n/a
4	MAFK	chr2:152146167-152146811	HepG2	liver:	n/a	n/a
5	MAX	chr2:152144726-152146773	K562	blood:	n/a	n/a
6	HCFC1	chr2:152145811-152146725	K562	blood:	n/a	n/a
7	STAT5A	chr2:152146168-152146801	GM12878	blood:	n/a	chr2:152146448-152146459
8	GTF2F1	chr2:152146198-152146910	Hela-S3	cervix:	n/a	n/a
9	MTA3	chr2:152145693-152146893	GM12878	blood:	n/a	n/a
10	IRF1	chr2:152145789-152147063	K562	blood:	n/a	chr2:152146446-152146460 chr2:152146443-152146457 chr2:152146442-152146455 chr2:152146436-152146452 chr2:152146447-152146460 chr2:152146442-152146455 chr2:152146442-152146456 chr2:152145826-152145836 chr2:152146973-152146982 chr2:152146445-152146459 chr2:152146972-152146981 chr2:152145822-152145839 chr2:152145822-152145836 chr2:152146443-152146453 chr2:152146441-152146461 chr2:152146445-152146462 chr2:152146442-152146455 chr2:152146437-152146458 chr2:152145825-152145838 chr2:152146437-152146454 chr2:152145826-152145840
11	STAT3	chr2:152146002-152147365	MCF10A-Er-Src	breast:	n/a	chr2:152146448-152146459
12	FOXA1	chr2:152146543-152146813	T-47D	breast:	n/a	n/a
13	MAX	chr2:152144461-152146836	NB4	blood:	n/a	n/a
14	TCF7L2	chr2:152146615-152146885	MCF-7	breast:	n/a	chr2:152146861-152146868
15	POLR2A	chr2:152144649-152146924	GM19193	blood:	n/a	n/a
16	YY1	chr2:152146639-152146823	K562	blood:	n/a	n/a
17	EBF1	chr2:152145835-152146907	GM12878	blood:	n/a	n/a
18	STAT3	chr2:152145817-152147256	MCF10A-Er-Src	breast:	n/a	chr2:152145825-152145836 chr2:152146448-152146459
19	POLR2A	chr2:152144627-152146832	GM18951	blood:	n/a	n/a
20	CEBPB	chr2:152146298-152146868	K562	blood:	n/a	n/a
21	POLR2A	chr2:152144619-152146929	GM18505	blood:	n/a	n/a
22	POLR2A	chr2:152145723-152146957	HL-60	blood:	n/a	n/a
23	ZNF384	chr2:152144790-152147390	K562	blood:	n/a	n/a
24	TCF7L2	chr2:152145903-152146872	Hela-S3	cervix:	n/a	chr2:152146861-152146868
25	MAX	chr2:152145241-152146892	Hela-S3	cervix:	n/a	n/a
26	STAT2	chr2:152145788-152146892	K562	blood:	n/a	chr2:152146428-152146443 chr2:152145825-152145836 chr2:152146445-152146460 chr2:152146448-152146459
27	STAT3	chr2:152146160-152146886	Hela-S3	cervix:	n/a	chr2:152146448-152146459
28	POLR2A	chr2:152145059-152146848	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr2:152146604-152146875	GM12891	blood:	n/a	n/a
30	TAF1	chr2:152145737-152146869	GM12878	blood:	n/a	n/a
31	TFAP2C	chr2:152145803-152147026	Hela-S3	cervix:	n/a	chr2:152146723-152146738
32	FOXM1	chr2:152145988-152146741	GM12878	blood:	n/a	n/a
33	FOXM1	chr2:152145708-152146864	GM12878	blood:	n/a	n/a
34	STAT1	chr2:152145870-152146813	K562	blood:	n/a	chr2:152146154-152146165 chr2:152146448-152146459
35	STAT1	chr2:152145982-152146822	K562	blood:	n/a	chr2:152146154-152146165 chr2:152146448-152146459
36	POLR2A	chr2:152145555-152147082	MCF10A-Er-Src	breast:	n/a	n/a
37	TBP	chr2:152145877-152146786	HepG2	liver:	n/a	n/a
38	UBTF	chr2:152145714-152146976	K562	blood:	n/a	n/a
39	MAFF	chr2:152146189-152146784	HepG2	liver:	n/a	n/a
40	POLR2A	chr2:152145625-152146838	GM12892	blood:	n/a	n/a
41	ZMIZ1	chr2:152145835-152146901	K562	blood:	n/a	n/a
42	POLR2A	chr2:152145017-152147109	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr2:152145840-152146747	GM12878	blood:	n/a	n/a
44	MAZ	chr2:152145831-152146949	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:152145676-152146861	HUVEC	blood vessel:	n/a	n/a
46	MAFK	chr2:152146111-152146811	IMR90	lung:	n/a	n/a
47	POLR2A	chr2:152143888-152147400	GM12891	blood:	n/a	n/a
48	POLR2A	chr2:152143917-152147179	PBDE	blood:	n/a	n/a
49	SIN3AK20	chr2:152145698-152147027	MCF-7	breast:	n/a	n/a
50	STAT3	chr2:152146001-152147225	MCF10A-Er-Src	breast:	n/a	chr2:152146448-152146459

No.	Distal block	Cell Line	Cell type
1	chr2:152116868..152120610-chr2:152144685..152147660,4	MCF-7	breast:
2	chr2:152145011..152148288-chr2:152265460..152267609,4	MCF-7	breast:
3	chr2:152117973..152120026-chr2:152143620..152147532,3	K562	blood:
4	chr2:152144813..152149803-chr2:152261382..152268379,11	K562	blood:
5	chr2:152146182..152146803-chr2:152266084..152266913,2	MCF-7	breast:
6	chr2:152115426..152120009-chr2:152142898..152146726,5	K562	blood:
7	chr2:152117804..152120182-chr2:152144785..152147621,2	MCF-7	breast:
8	chr2:152144798..152147073-chr2:152265350..152268359,5	MCF-7	breast:

Variant related genes	Relation type
NMI	TF binding region
ENSG00000080345	Chromatin interaction
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10167886	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10169816	0.89[EUR][1000 genomes]
rs10174715	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10182245	0.89[EUR][1000 genomes]
rs10187344	0.82[EUR][1000 genomes]
rs1023634	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10490522	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10490523	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11679466	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12465426	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12617669	0.88[EUR][1000 genomes]
rs12617724	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2551671	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2880489	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs289828	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs289829	0.82[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs289832	0.89[EUR][1000 genomes]
rs289833	0.88[EUR][1000 genomes]
rs289835	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34132424	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35058039	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35499578	0.84[EUR][1000 genomes]
rs3771886	0.82[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs3771887	0.82[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs3771888	0.82[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs387297	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs403411	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4664021	0.94[ASN][1000 genomes]
rs4665159	0.89[EUR][1000 genomes]
rs6433327	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6708382	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs6715393	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6715902	0.81[ASN][1000 genomes]
rs6718415	0.89[EUR][1000 genomes]
rs6719213	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6726634	0.86[CHB][hapmap]
rs6747782	0.81[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6751802	0.82[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs6757821	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs7574216	0.94[ASN][1000 genomes]
rs7585805	0.91[ASN][1000 genomes]
rs9287955	0.86[CHB][hapmap]
rs9287956	0.86[CHB][hapmap]
rs9636292	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
9	esv1793984	chr2:152138749-152154163	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2278089	STAM2	cis	parietal	SCAN
rs2278089	RIF1	cis	parietal	SCAN
rs2278089	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs2278089	RBM43	cis	parietal	SCAN
rs2278089	RND3	cis	cerebellum	SCAN
rs2278089	TNFAIP6	cis	Whole Blood	GTEx
rs2278089	TNFAIP6	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152144400-152146800	Active TSS	A549	lung
2	chr2:152144400-152147200	Active TSS	GM12878-XiMat	blood
3	chr2:152144800-152147000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:152144800-152147000	Active TSS	Rectal Smooth Muscle	rectum
5	chr2:152144800-152147000	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr2:152144800-152147200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr2:152145000-152147200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:152145200-152146800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:152145200-152146800	Active TSS	Right Ventricle	heart
10	chr2:152145200-152147000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:152145200-152147000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:152145200-152147000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:152145200-152147000	Active TSS	Brain Cingulate Gyrus	brain
14	chr2:152145200-152147000	Active TSS	Brain Hippocampus Middle	brain
15	chr2:152145200-152147000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr2:152145200-152147000	Active TSS	Brain Substantia Nigra	brain
17	chr2:152145200-152147000	Active TSS	Colon Smooth Muscle	Colon
18	chr2:152145200-152147000	Active TSS	Duodenum Mucosa	Duodenum
19	chr2:152145200-152147000	Active TSS	Psoas Muscle	Psoas
20	chr2:152145200-152147000	Active TSS	Right Atrium	heart
21	chr2:152145200-152147000	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr2:152145200-152147000	Active TSS	Stomach Smooth Muscle	stomach
23	chr2:152145200-152147000	Active TSS	Hela-S3	cervix
24	chr2:152145200-152147000	Active TSS	HSMMtube	muscle
25	chr2:152145200-152147000	Active TSS	Osteobl	bone
26	chr2:152145200-152147200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr2:152145200-152147200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:152145400-152146800	Active TSS	Primary T cells from cord blood	blood
29	chr2:152145400-152146800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:152145400-152146800	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:152145400-152146800	Active TSS	Adipose Nuclei	Adipose
32	chr2:152145400-152146800	Active TSS	Liver	Liver
33	chr2:152145400-152146800	Active TSS	Esophagus	oesophagus
34	chr2:152145400-152146800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr2:152145400-152146800	Active TSS	Fetal Lung	lung
36	chr2:152145400-152146800	Active TSS	Gastric	stomach
37	chr2:152145400-152146800	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr2:152145400-152146800	Active TSS	Small Intestine	intestine
39	chr2:152145400-152146800	Active TSS	Stomach Mucosa	stomach
40	chr2:152145400-152146800	Active TSS	Dnd41	blood
41	chr2:152145400-152146800	Active TSS	K562	blood
42	chr2:152145400-152147000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:152145400-152147000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr2:152145400-152147000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr2:152145400-152147000	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr2:152145400-152147000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:152145400-152147000	Active TSS	Aorta	Aorta
48	chr2:152145400-152147000	Active TSS	Brain Anterior Caudate	brain
49	chr2:152145400-152147000	Active TSS	Colonic Mucosa	Colon
50	chr2:152145400-152147000	Active TSS	Fetal Intestine Large	intestine

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