Variant report

Variant	rs805310
Chromosome Location	chr2:54196238-54196239
allele	A/G
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	POLR2A	chr2:54195426-54199062	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL1	chr2:54196211-54196901	HCT-116	colon:	n/a	chr2:54196588-54196596 chr2:54196588-54196596 chr2:54196584-54196595 chr2:54196589-54196596 chr2:54196587-54196597
3	SIN3A	chr2:54196218-54196603	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFIC	chr2:54196219-54196893	HepG2	liver:	n/a	n/a
5	BACH1	chr2:54196166-54196826	K562	blood:	n/a	chr2:54196585-54196599
6	POLR2A	chr2:54195526-54196830	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:54195490-54199155	PBDE	blood:	n/a	n/a
8	TBL1XR1	chr2:54196197-54197202	K562	blood:	n/a	n/a
9	CTCF	chr2:54196220-54196370	HPF	lung:	n/a	n/a
10	SIN3AK20	chr2:54196210-54197028	MCF-7	breast:	n/a	n/a
11	MXI1	chr2:54196016-54199237	IMR90	lung:	n/a	n/a
12	TCF12	chr2:54196235-54196970	A549	lung:	n/a	n/a
13	MBD4	chr2:54196224-54196855	HepG2	liver:	n/a	n/a
14	FOXA2	chr2:54195632-54197176	HepG2	liver:	n/a	n/a
15	FOSL2	chr2:54196185-54196925	A549	lung:	n/a	chr2:54196587-54196598 chr2:54196588-54196596 chr2:54196588-54196596 chr2:54196584-54196595 chr2:54196589-54196596 chr2:54196587-54196597
16	CHD1	chr2:54195365-54199244	IMR90	lung:	n/a	n/a
17	JUN	chr2:54196185-54196810	K562	blood:	n/a	chr2:54196588-54196596 chr2:54196588-54196596 chr2:54196584-54196595 chr2:54196589-54196596 chr2:54196587-54196597
18	JUN	chr2:54195869-54197641	K562	blood:	n/a	chr2:54196588-54196596 chr2:54196588-54196596 chr2:54196584-54196595 chr2:54196589-54196596 chr2:54196587-54196597
19	MAZ	chr2:54196115-54199037	IMR90	lung:	n/a	chr2:54196587-54196596
20	MXI1	chr2:54195676-54199239	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54165576..54167252-chr2:54193257..54196468,3	K562	blood:
2	chr2:54195012..54197478-chr2:54219368..54222229,2	K562	blood:
3	chr2:54185625..54188123-chr2:54194333..54197670,3	MCF-7	breast:
4	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
5	chr2:54184275..54188127-chr2:54193177..54197889,6	K562	blood:
6	chr2:54157567..54166967-chr2:54194910..54201681,12	MCF-7	breast:
7	chr2:54196188..54197004-chr20:2451334..2451980,2	NB4	blood:
8	chr2:54176939..54180611-chr2:54194148..54196574,3	K562	blood:
9	chr2:54195961..54197468-chr2:54240342..54242610,2	MCF-7	breast:
10	chr2:54194885..54197429-chr2:55459526..55461126,2	MCF-7	breast:
11	chr2:54194904..54197235-chr2:54307312..54309509,2	K562	blood:

Variant related genes	Relation type
ACYP2	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000125835	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000241114	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10167891	0.87[ASN][1000 genomes]
rs10168293	0.97[ASN][1000 genomes]
rs10183655	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs11674724	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11683741	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11689025	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11694711	0.96[ASN][1000 genomes]
rs11890838	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11893270	0.80[ASN][1000 genomes]
rs11898855	0.80[AMR][1000 genomes]
rs13394278	0.87[ASN][1000 genomes]
rs1477258	0.84[ASN][1000 genomes]
rs17045452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17045474	0.87[CHB][hapmap]
rs17045488	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2112122	0.81[ASN][1000 genomes]
rs2253760	0.83[CHB][hapmap]
rs2287643	0.83[CHB][hapmap]
rs2302879	0.83[AMR][1000 genomes]
rs2542571	0.82[CHB][hapmap]
rs2542575	0.83[CHB][hapmap]
rs2692516	0.87[CHB][hapmap]
rs2692534	0.84[CEU][hapmap];0.87[CHB][hapmap]
rs28653587	0.87[ASN][1000 genomes]
rs28851028	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2909459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2949815	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731967	0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs4671742	0.94[ASN][1000 genomes]
rs4671746	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4671747	0.83[ASN][1000 genomes]
rs55692047	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56302494	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62139336	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6545377	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545380	0.81[ASN][1000 genomes]
rs6545381	0.81[AMR][1000 genomes]
rs66773232	0.93[ASN][1000 genomes]
rs6714450	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6715488	0.86[ASN][1000 genomes]
rs6746965	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs6748976	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6748997	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs698855	0.91[CHB][hapmap]
rs698857	0.81[AMR][1000 genomes]
rs72799298	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72904908	0.87[ASN][1000 genomes]
rs7559384	0.81[AMR][1000 genomes]
rs7559947	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564912	0.87[ASN][1000 genomes]
rs7591431	0.87[ASN][1000 genomes]
rs805312	0.83[AMR][1000 genomes]
rs805313	0.83[AMR][1000 genomes]
rs805314	0.80[AMR][1000 genomes]
rs805315	0.80[AMR][1000 genomes]
rs805319	0.83[AMR][1000 genomes]
rs805321	0.92[CHB][hapmap];0.83[AMR][1000 genomes]
rs805323	0.83[AMR][1000 genomes]
rs805328	0.90[CHB][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs805329	0.81[AMR][1000 genomes]
rs805334	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs805344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805346	0.83[AMR][1000 genomes]
rs805347	0.83[AMR][1000 genomes]
rs805348	0.81[AMR][1000 genomes]
rs805349	0.81[AMR][1000 genomes]
rs805351	0.92[CHB][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs805352	0.91[CHB][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs805354	0.87[AMR][1000 genomes]
rs805355	0.87[AMR][1000 genomes]
rs805356	0.87[AMR][1000 genomes]
rs805357	0.87[AMR][1000 genomes]
rs805362	0.87[AMR][1000 genomes]
rs805363	0.83[AMR][1000 genomes]
rs805365	0.91[CHB][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs805384	0.83[AMR][1000 genomes]
rs805386	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs805394	0.80[AMR][1000 genomes]
rs805397	0.83[AMR][1000 genomes]
rs805399	0.91[CHB][hapmap];0.81[AMR][1000 genomes]
rs805400	0.81[AMR][1000 genomes]
rs805401	0.91[CHB][hapmap];0.83[AMR][1000 genomes]
rs805404	0.91[CHB][hapmap];0.83[AMR][1000 genomes]
rs805406	0.81[AMR][1000 genomes]
rs805407	0.81[AMR][1000 genomes]
rs805408	0.92[CHB][hapmap];0.81[AMR][1000 genomes]
rs805409	0.80[AMR][1000 genomes]
rs805411	0.81[AMR][1000 genomes]
rs805414	0.81[AMR][1000 genomes]
rs805415	0.80[AMR][1000 genomes]
rs805419	0.80[AMR][1000 genomes]
rs805420	0.80[AMR][1000 genomes]
rs805425	0.81[AMR][1000 genomes]
rs805426	0.91[CHB][hapmap]
rs805428	0.80[AMR][1000 genomes]
rs805429	0.80[AMR][1000 genomes]
rs805447	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs805452	0.82[AFR][1000 genomes]
rs809282	0.81[AMR][1000 genomes]
rs9631059	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs805310	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54189800-54196400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:54190000-54196400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:54190400-54197000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:54190600-54196400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:54190600-54197000	Weak transcription	Esophagus	oesophagus
6	chr2:54192600-54196400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:54192600-54197000	Weak transcription	Spleen	Spleen
8	chr2:54193600-54196400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:54194000-54197000	Weak transcription	Gastric	stomach
10	chr2:54194000-54198800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr2:54194200-54196600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr2:54194400-54196600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:54194400-54197000	Flanking Active TSS	Dnd41	blood
14	chr2:54194800-54198800	Active TSS	Osteobl	bone
15	chr2:54194800-54199400	Active TSS	HSMMtube	muscle
16	chr2:54195000-54196400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:54195000-54196800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:54195000-54198800	Active TSS	HMEC	breast
19	chr2:54195000-54199200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr2:54195000-54199400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:54195200-54196400	Flanking Active TSS	Liver	Liver
22	chr2:54195200-54197000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:54195200-54197400	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr2:54195200-54199200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:54195200-54199400	Active TSS	HSMM	muscle
26	chr2:54195400-54196400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:54195400-54196400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:54195400-54196400	Enhancers	Fetal Intestine Large	intestine
29	chr2:54195400-54196400	Flanking Active TSS	A549	lung
30	chr2:54195400-54196600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr2:54195400-54197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:54195400-54197000	Weak transcription	Lung	lung
33	chr2:54195400-54197000	Weak transcription	Pancreas	Pancrea
34	chr2:54195400-54197200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr2:54195400-54197400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr2:54195400-54198000	Active TSS	Right Atrium	heart
37	chr2:54195400-54198600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:54195400-54199000	Active TSS	Left Ventricle	heart
39	chr2:54195400-54199000	Active TSS	Right Ventricle	heart
40	chr2:54195400-54199200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:54195400-54199200	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr2:54195400-54199200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr2:54195400-54199200	Active TSS	Psoas Muscle	Psoas
44	chr2:54195400-54199400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:54195600-54196400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:54195600-54196400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr2:54195600-54196400	Enhancers	Fetal Intestine Small	intestine
48	chr2:54195600-54196400	Flanking Active TSS	Fetal Lung	lung
49	chr2:54195600-54196400	Flanking Active TSS	Thymus	Thymus
50	chr2:54195600-54196600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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