Variant report

Variant	rs11123849
Chromosome Location	chr2:98286235-98286236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr2:98285990-98286294	K562	blood:	n/a	chr2:98286130-98286141 chr2:98286129-98286142 chr2:98286130-98286141
2	POLR2A	chr2:98285893-98286316	GM12891	blood:	n/a	n/a
3	MAZ	chr2:98286144-98286273	K562	blood:	n/a	n/a
4	ELF1	chr2:98285892-98286301	GM12878	blood:	n/a	chr2:98286130-98286141 chr2:98286129-98286142 chr2:98286130-98286141
5	SPI1	chr2:98285907-98286273	GM12891	blood:	n/a	n/a
6	MAZ	chr2:98286219-98286369	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:98285800-98286436	GM12891	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98278667..98281978-chr2:98283382..98286512,4	K562	blood:
2	chr2:98260499..98265219-chr2:98284794..98288071,4	MCF-7	breast:

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZAP70-2	chr2:98286206-98286297	ENSG00000228486.2
2	lnc-ZAP70-2	chr2:98286209-98286297	ENSG00000228486.2
3	lnc-ZAP70-2	chr2:98286153-98286297	ENSG00000228486.5
4	lnc-ZAP70-2	chr2:98285871-98286297	NONHSAT072667
5	lnc-ZAP70-2	chr2:98286176-98286297	ENSG00000228486.5
6	lnc-ZAP70-2	chr2:98285643-98286297	ENSG00000228486.5
7	lnc-ZAP70-2	chr2:98286153-98286297	ENSG00000228486.5
8	lnc-ZAP70-2	chr2:98286206-98286297	NR_038386

No data

Variant related genes	Relation type
LINC01125	TF binding region
ENSG00000135940	Chromatin interaction
ENSG00000201806	Chromatin interaction
ENSG00000115073	Chromatin interaction
ENSG00000228486	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs1020396	0.81[CHB][hapmap]
rs1042705	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496323	0.81[CHB][hapmap]
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];0.86[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.97[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];0.82[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12991969	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001139	0.93[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	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034349	0.81[CHB][hapmap]
rs1375436	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463174	0.81[CHB][hapmap]
rs1470625	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550995	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2053824	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]
rs2167007	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276644	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276645	0.81[CHB][hapmap]
rs2290124	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3474	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542980	0.89[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];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11123849	ZAP70	cis	cerebellum	SCAN
rs11123849	ANKRD36B	cis	Artery Tibial	GTEx
rs11123849	INPP4A	cis	cerebellum	SCAN
rs11123849	ACTR1B	cis	cerebellum	SCAN
rs11123849	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs11123849	ANKRD36B	cis	Nerve Tibial	GTEx
rs11123849	ANKRD36B	cis	Thyroid	GTEx
rs11123849	ANKRD39	cis	cerebellum	SCAN
rs11123849	ANKRD36B	cis	cerebellum	SCAN
rs11123849	ZAP70	cis	Nerve Tibial	GTEx
rs11123849	ANKRD36B	cis	lung	GTEx
rs11123849	CNNM3	cis	cerebellum	SCAN

Chromatin state (count:40 , 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	chr2:98281200-98289600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:98281400-98287200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:98281400-98289400	Weak transcription	Lung	lung
6	chr2:98281400-98290000	Weak transcription	Left Ventricle	heart
7	chr2:98281400-98295200	Weak transcription	Esophagus	oesophagus
8	chr2:98281600-98287000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:98281600-98287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:98281600-98288000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:98281600-98288800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:98281600-98289600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:98281600-98289600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:98281600-98289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:98281600-98290000	Weak transcription	Fetal Intestine Small	intestine
16	chr2:98281600-98290200	Weak transcription	Pancreas	Pancrea
17	chr2:98281600-98290400	Weak transcription	Thymus	Thymus
18	chr2:98281600-98291400	Weak transcription	Right Atrium	heart
19	chr2:98281600-98292000	Weak transcription	Adipose Nuclei	Adipose
20	chr2:98281600-98292800	Weak transcription	HSMM	muscle
21	chr2:98281600-98293200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:98281600-98294800	Weak transcription	Brain Anterior Caudate	brain
23	chr2:98281600-98295400	Weak transcription	Right Ventricle	heart
24	chr2:98281600-98298800	Weak transcription	Aorta	Aorta
25	chr2:98281800-98289000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:98281800-98289200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:98281800-98289600	Weak transcription	GM12878-XiMat	blood
28	chr2:98281800-98293800	Weak transcription	Brain Angular Gyrus	brain
29	chr2:98281800-98296200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:98281800-98296200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:98282000-98287600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:98282000-98290000	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:98282000-98292000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:98282000-98293800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:98284400-98286400	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:98285000-98286400	Strong transcription	Fetal Stomach	stomach
37	chr2:98285600-98292200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:98285800-98286800	Enhancers	Primary B cells from peripheral blood	blood
39	chr2:98286200-98286400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:98286200-98292000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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