Variant report

Variant	rs2053824
Chromosome Location	chr2:98281634-98281635
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	TBL1XR1	chr2:98280464-98281818	K562	blood:	n/a	n/a
2	POLR2A	chr2:98278016-98282070	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:98279158-98281635	PBDE	blood:	n/a	n/a
4	CHD1	chr2:98278816-98281671	IMR90	lung:	n/a	chr2:98280105-98280115
5	CTCF	chr2:98278862-98281848	SK-N-SH	brain:	n/a	chr2:98280555-98280563 chr2:98280387-98280400 chr2:98279033-98279046 chr2:98279295-98279308
6	RFX5	chr2:98278853-98281707	SK-N-SH	brain:	n/a	chr2:98280645-98280659
7	MAFF	chr2:98280923-98281777	K562	blood:	n/a	n/a
8	POLR2A	chr2:98278623-98281994	K562	blood:	n/a	n/a
9	POLR2A	chr2:98281439-98282031	K562	blood:	n/a	n/a
10	JUND	chr2:98280393-98281930	SK-N-SH	brain:	n/a	chr2:98280407-98280416 chr2:98280411-98280420
11	ZKSCAN1	chr2:98281545-98281737	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:98278923-98281723	Hela-S3	cervix:	n/a	n/a
13	RCOR1	chr2:98280460-98281678	K562	blood:	n/a	n/a
14	MYC	chr2:98278994-98281708	K562	blood:	n/a	chr2:98280224-98280234 chr2:98279386-98279396
15	NRF1	chr2:98280076-98281648	SK-N-SH	brain:	n/a	chr2:98280224-98280233 chr2:98280585-98280594
16	KAP1	chr2:98280604-98281645	U2OS	brain:	n/a	n/a
17	ZNF263	chr2:98278962-98281671	HEK293-T-REx	kidney:	n/a	n/a
18	JUN	chr2:98278899-98282137	K562	blood:	n/a	chr2:98280407-98280416 chr2:98279470-98279477 chr2:98280411-98280420 chr2:98279375-98279383 chr2:98279468-98279477 chr2:98280674-98280687 chr2:98279373-98279384 chr2:98279468-98279478 chr2:98279468-98279478 chr2:98280223-98280232

No.	Distal block	Cell Line	Cell type
1	chr2:98205848..98207835-chr2:98279004..98283186,3	MCF-7	breast:
2	chr2:98279310..98282281-chr2:98310556..98313961,3	MCF-7	breast:
3	chr2:98279912..98282586-chr2:98290130..98292098,3	K562	blood:
4	chr2:98278667..98281978-chr2:98283382..98286512,4	K562	blood:
5	chr2:98279513..98282179-chr2:98292256..98296228,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZAP70-2	chr2:98280748-98282910	NONHSAT072664

Variant related genes	Relation type
ACTR1B	TF binding region
RNU4-8P	TF binding region
LINC01125	TF binding region
ENSG00000228486	Chromatin interaction
ENSG00000196912	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1020396	0.81[CHB][hapmap]
rs1042705	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496323	0.81[CHB][hapmap]
rs11123849	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680855	0.81[CHB][hapmap]
rs11893601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11894651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12991969	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001139	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13001728	0.81[CEU][hapmap]
rs13003963	0.91[ASN][1000 genomes]
rs13009163	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034349	0.81[CHB][hapmap]
rs1375436	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463174	0.81[CHB][hapmap]
rs1470625	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550995	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2167007	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276644	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276645	0.81[CHB][hapmap]
rs2290124	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3474	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542980	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs873886	0.95[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv431402	chr2:97669032-98281634	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1005846	chr2:97972600-98281634	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv1009263	chr2:98013814-98281634	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv3435324	chr2:98279520-98282118	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2053824	ANKRD36B	cis	cerebellum	SCAN
rs2053824	ANKRD36B	cis	Nerve Tibial	GTEx
rs2053824	ZAP70	cis	Nerve Tibial	GTEx
rs2053824	ANKRD39	cis	cerebellum	SCAN
rs2053824	ANKRD36B	cis	lung	GTEx
rs2053824	CNNM3	cis	cerebellum	SCAN
rs2053824	INPP4A	cis	cerebellum	SCAN
rs2053824	ANKRD36B	cis	Artery Tibial	GTEx
rs2053824	ANKRD36B	cis	Thyroid	GTEx
rs2053824	ACTR1B	cis	cerebellum	SCAN
rs2053824	ZAP70	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98279200-98281800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:98279200-98281800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:98279200-98281800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:98279400-98281800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:98279400-98281800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:98279400-98282000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:98279800-98281800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:98279800-98281800	Active TSS	NHEK	skin
9	chr2:98279800-98282000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:98280000-98281800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:98281000-98290400	Weak transcription	Spleen	Spleen
12	chr2:98281000-98323800	Weak transcription	Gastric	stomach
13	chr2:98281200-98281800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr2:98281200-98281800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:98281200-98281800	Flanking Active TSS	Dnd41	blood
16	chr2:98281200-98281800	Flanking Active TSS	Hela-S3	cervix
17	chr2:98281200-98289600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:98281400-98281800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr2:98281400-98281800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr2:98281400-98281800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:98281400-98281800	Flanking Active TSS	A549	lung
22	chr2:98281400-98281800	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:98281400-98281800	Flanking Active TSS	HMEC	breast
24	chr2:98281400-98282000	Flanking Active TSS	K562	blood
25	chr2:98281400-98287200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:98281400-98289400	Weak transcription	Lung	lung
27	chr2:98281400-98290000	Weak transcription	Left Ventricle	heart
28	chr2:98281400-98295200	Weak transcription	Esophagus	oesophagus
29	chr2:98281600-98281800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr2:98281600-98281800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:98281600-98281800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:98281600-98281800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:98281600-98281800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:98281600-98281800	Enhancers	Primary B cells from cord blood	blood
35	chr2:98281600-98281800	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr2:98281600-98281800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:98281600-98281800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr2:98281600-98281800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:98281600-98281800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr2:98281600-98281800	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr2:98281600-98281800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:98281600-98281800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:98281600-98281800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:98281600-98281800	Enhancers	Brain Angular Gyrus	brain
45	chr2:98281600-98281800	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:98281600-98281800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr2:98281600-98281800	Enhancers	Brain Substantia Nigra	brain
48	chr2:98281600-98281800	Enhancers	Colon Smooth Muscle	Colon
49	chr2:98281600-98281800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr2:98281600-98281800	Active TSS	Rectal Mucosa Donor 29	rectum

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