Variant report

Variant	rs6745653
Chromosome Location	chr2:98289997-98289998
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	MAZ	chr2:98289648-98290809	K562	blood:	n/a	chr2:98290432-98290441
2	HMGN3	chr2:98289880-98290729	K562	blood:	n/a	n/a
3	TBP	chr2:98289870-98290350	K562	blood:	n/a	n/a
4	ATF1	chr2:98289774-98290894	K562	blood:	n/a	n/a
5	CEBPD	chr2:98289991-98290393	K562	blood:	n/a	n/a
6	POLR2A	chr2:98289603-98290667	K562	blood:	n/a	n/a
7	MAX	chr2:98289605-98290405	K562	blood:	n/a	n/a
8	TBL1XR1	chr2:98289858-98290732	K562	blood:	n/a	n/a
9	MAFK	chr2:98289908-98290587	K562	blood:	n/a	n/a
10	NRF1	chr2:98289911-98290039	GM12878	blood:	n/a	n/a
11	TEAD4	chr2:98289991-98290444	K562	blood:	n/a	n/a
12	UBTF	chr2:98289659-98290738	K562	blood:	n/a	n/a
13	POLR2A	chr2:98289675-98290632	K562	blood:	n/a	n/a
14	CBX3	chr2:98289713-98290370	K562	blood:	n/a	n/a
15	JUND	chr2:98289605-98290765	K562	blood:	n/a	chr2:98289770-98289781 chr2:98289771-98289780 chr2:98289773-98289780
16	CTCF	chr2:98289900-98290050	HepG2	liver:	n/a	n/a
17	CUX1	chr2:98289765-98290963	K562	blood:	n/a	n/a
18	POLR2A	chr2:98289956-98290374	K562	blood:	n/a	n/a
19	TAL1	chr2:98289985-98290702	K562	blood:	n/a	n/a
20	RCOR1	chr2:98289690-98290801	K562	blood:	n/a	n/a
21	CHD2	chr2:98289973-98290358	K562	blood:	n/a	n/a
22	NR2F2	chr2:98289984-98290560	K562	blood:	n/a	n/a
23	CCNT2	chr2:98289981-98290644	K562	blood:	n/a	chr2:98290258-98290278
24	NR2F2	chr2:98289851-98290822	K562	blood:	n/a	n/a
25	BHLHE40	chr2:98289690-98290897	K562	blood:	n/a	n/a
26	GATA2	chr2:98289955-98290423	K562	blood:	n/a	chr2:98290267-98290276 chr2:98290258-98290275 chr2:98290267-98290277 chr2:98290265-98290278 chr2:98290269-98290276
27	MAX	chr2:98289707-98290601	K562	blood:	n/a	chr2:98290432-98290441
28	EP300	chr2:98289994-98290858	K562	blood:	n/a	chr2:98290829-98290836 chr2:98290140-98290147
29	TEAD4	chr2:98289913-98290881	K562	blood:	n/a	n/a
30	RCOR1	chr2:98289705-98290495	K562	blood:	n/a	n/a
31	POLR2A	chr2:98289977-98290387	K562	blood:	n/a	n/a
32	TBL1XR1	chr2:98289664-98290516	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:98286306..98287909-chr2:98288768..98291732,2	MCF-7	breast:
2	chr2:98277540..98280673-chr2:98288354..98290107,4	K562	blood:
3	chr2:98261015..98264268-chr2:98289158..98291782,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZAP70-2	chr2:98289635-98292184	NONHSAT072675
2	lnc-ZAP70-2	chr2:98289635-98291020	NONHSAT072676

Variant related genes	Relation type
LINC01125	TF binding region
ENSG00000228486	Chromatin interaction
ENSG00000135940	Chromatin interaction
ENSG00000115073	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11886025	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886239	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904110	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17841861	1.00[CEU][hapmap]
rs3475	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55981050	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59134572	0.92[ASN][1000 genomes]
rs6543021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951131	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73959752	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73959753	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73959769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73959786	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73959787	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	esv3451326	chr2:98289174-98304076	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98281000-98290400	Weak transcription	Spleen	Spleen
2	chr2:98281000-98323800	Weak transcription	Gastric	stomach
3	chr2:98281400-98290000	Weak transcription	Left Ventricle	heart
4	chr2:98281400-98295200	Weak transcription	Esophagus	oesophagus
5	chr2:98281600-98290000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:98281600-98290200	Weak transcription	Pancreas	Pancrea
7	chr2:98281600-98290400	Weak transcription	Thymus	Thymus
8	chr2:98281600-98291400	Weak transcription	Right Atrium	heart
9	chr2:98281600-98292000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:98281600-98292800	Weak transcription	HSMM	muscle
11	chr2:98281600-98293200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:98281600-98294800	Weak transcription	Brain Anterior Caudate	brain
13	chr2:98281600-98295400	Weak transcription	Right Ventricle	heart
14	chr2:98281600-98298800	Weak transcription	Aorta	Aorta
15	chr2:98281800-98293800	Weak transcription	Brain Angular Gyrus	brain
16	chr2:98281800-98296200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:98281800-98296200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:98282000-98290000	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:98282000-98292000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:98282000-98293800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:98285600-98292200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:98286200-98292000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:98288600-98293600	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:98289200-98290000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:98289200-98291600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:98289200-98292000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:98289400-98290400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:98289400-98292200	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:98289600-98290000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:98289600-98290400	Enhancers	Fetal Thymus	thymus
31	chr2:98289600-98290400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr2:98289600-98291600	Enhancers	GM12878-XiMat	blood
33	chr2:98289800-98290600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr2:98289800-98291000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:98289800-98291000	Flanking Active TSS	K562	blood
36	chr2:98289800-98293600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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