Variant report

Variant	rs11680855
Chromosome Location	chr2:98317685-98317686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:12)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:98313545..98315394-chr2:98316624..98319251,2	MCF-7	breast:
2	chr2:98317619..98320456-chr2:98324086..98325839,2	MCF-7	breast:
3	chr2:98279781..98283604-chr2:98316851..98320618,5	K562	blood:
4	chr2:98277866..98283604-chr2:98316329..98321534,8	K562	blood:
5	chr2:98317266..98319874-chr2:98357687..98360540,2	K562	blood:

(count:12 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZAP70-2	chr2:98317617-98317787	ENSG00000228486.2
2	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.2
3	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
4	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
5	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
6	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
7	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
8	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
9	lnc-ZAP70-2	chr2:98317617-98317760	ENSG00000228486.5
10	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
11	lnc-ZAP70-2	chr2:98317617-98317767	ENSG00000228486.5
12	lnc-ZAP70-2	chr2:98317617-98317767	NR_038386

No data

Variant related genes	Relation type
ENSG00000228486	Chromatin interaction
ENSG00000115073	Chromatin interaction
ENSG00000201806	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1020396	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1042705	0.81[CHB][hapmap]
rs10496323	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123849	0.81[CHB][hapmap]
rs11123861	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11547232	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11690658	0.96[CEU][hapmap]
rs11691779	0.87[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap]
rs11893601	0.81[CHB][hapmap]
rs11894651	0.81[CHB][hapmap]
rs12994535	0.96[CEU][hapmap]
rs12994966	0.96[ASN][1000 genomes]
rs12997695	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13000505	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13001728	1.00[CEU][hapmap]
rs13003963	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13034349	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1463173	0.96[CEU][hapmap];0.80[CHB][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1463174	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800649	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1823324	0.81[CHB][hapmap]
rs1965204	0.96[CEU][hapmap]
rs2053824	0.81[CHB][hapmap]
rs2276645	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2290124	0.81[CHB][hapmap]
rs35211079	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3931133	0.96[CEU][hapmap]
rs55772322	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56281704	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62157580	1.00[ASN][1000 genomes]
rs6718109	0.96[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap]

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	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
4	nsv874696	chr2:98309882-98362907	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv33510	chr2:98317103-98341302	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11680855	ZAP70	cis	lymphoblastoid	seeQTL
rs11680855	ANKRD36B	cis	lung	GTEx
rs11680855	ANKRD36B	cis	Thyroid	GTEx
rs11680855	ANKRD36B	cis	Artery Tibial	GTEx
rs11680855	ACTR1B	cis	cerebellum	SCAN
rs11680855	ANKRD36B	cis	Nerve Tibial	GTEx
rs11680855	AC017099.3	cis	Muscle Skeletal	GTEx
rs11680855	ZAP70	cis	cerebellum	SCAN
rs11680855	ANKRD39	cis	cerebellum	SCAN
rs11680855	ANKRD36B	cis	cerebellum	SCAN
rs11680855	ANKRD36B	cis	Skin Sun Exposed Lower leg	GTEx
rs11680855	CNNM3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98281000-98323800	Weak transcription	Gastric	stomach
2	chr2:98292200-98317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98306000-98322400	Weak transcription	Fetal Stomach	stomach
4	chr2:98309400-98317800	Weak transcription	HSMM	muscle
5	chr2:98312800-98324600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:98313800-98318000	Weak transcription	NHDF-Ad	bronchial
7	chr2:98313800-98318200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:98313800-98318400	Weak transcription	GM12878-XiMat	blood
9	chr2:98314000-98318200	Weak transcription	Osteobl	bone
10	chr2:98316400-98324000	Weak transcription	Pancreas	Pancrea
11	chr2:98316600-98319200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:98316800-98319200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:98317400-98317800	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:98317600-98318600	Enhancers	Fetal Muscle Trunk	muscle
15	chr2:98317600-98318600	Active TSS	Spleen	Spleen
16	chr2:98317600-98319600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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