Variant report

Variant	rs6719142
Chromosome Location	chr2:95830652-95830653
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	GABPA	chr2:95830511-95832081	MCF-7	breast:	n/a	chr2:95831532-95831546 chr2:95831155-95831162 chr2:95831535-95831544 chr2:95831535-95831546 chr2:95831535-95831549 chr2:95831161-95831168
2	REST	chr2:95830609-95832280	H1-neurons	neurons:	n/a	chr2:95831365-95831383 chr2:95831377-95831384
3	POLR2A	chr2:95830265-95831946	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:95830602-95832098	GM12891	blood:	n/a	n/a
5	MXI1	chr2:95830594-95832595	IMR90	lung:	n/a	n/a
6	POLR2A	chr2:95830629-95832107	PFSK-1	brain:	n/a	n/a
7	MAX	chr2:95830579-95832216	A549	lung:	n/a	n/a
8	TCF12	chr2:95830556-95832154	A549	lung:	n/a	chr2:95831186-95831193
9	STAT3	chr2:95830593-95831738	MCF10A-Er-Src	breast:	n/a	chr2:95831137-95831145 chr2:95831464-95831485 chr2:95831104-95831115
10	SIX5	chr2:95830593-95831913	A549	lung:	n/a	n/a
11	POLR2A	chr2:95830633-95832345	HepG2	liver:	n/a	n/a
12	HCFC1	chr2:95830573-95832437	Hela-S3	cervix:	n/a	n/a
13	MXI1	chr2:95830593-95832413	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr2:95830508-95832378	IMR90	lung:	n/a	n/a
15	GABPA	chr2:95830602-95831817	A549	lung:	n/a	chr2:95831532-95831546 chr2:95831155-95831162 chr2:95831535-95831544 chr2:95831535-95831546 chr2:95831535-95831549 chr2:95831161-95831168
16	SIN3A	chr2:95830641-95832161	H1-hESC	embryonic stem cell:	n/a	chr2:95831683-95831691

No.	Distal block	Cell Line	Cell type
1	chr2:95784064..95788692-chr2:95827645..95832682,10	MCF-7	breast:
2	chr2:95784303..95789114-chr2:95829766..95832778,9	MCF-7	breast:
3	chr2:95816122..95821729-chr2:95829524..95833130,7	MCF-7	breast:
4	chr2:95820602..95822831-chr2:95829587..95831468,2	MCF-7	breast:
5	chr2:95786108..95790506-chr2:95828555..95834084,9	K562	blood:
6	chr2:95829346..95831231-chr2:95961091..95963572,2	MCF-7	breast:
7	chr2:95830116..95832224-chr2:95974723..95976277,2	MCF-7	breast:
8	chr2:95786123..95790193-chr2:95829168..95832965,6	K562	blood:
9	chr2:95829966..95832262-chr2:95871285..95874374,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF514-1	chr2:95829476-95831182	NONHSAT072465

Variant related genes	Relation type
ZNF2	TF binding region
ENSG00000144029	Chromatin interaction
ENSG00000144026	Chromatin interaction
ENSG00000233757	Chromatin interaction
ENSG00000115041	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2113418	0.90[JPT][hapmap];0.83[YRI][hapmap]
rs3112226	0.88[ASN][1000 genomes]
rs3112989	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3112992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs3112994	0.95[ASN][1000 genomes]
rs3112998	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs889854	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][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	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6719142	ZNF514	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95826000-95830800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:95826200-95830800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:95826200-95830800	Weak transcription	Gastric	stomach
4	chr2:95826400-95830800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:95826400-95830800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:95829000-95830800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:95829000-95830800	Weak transcription	Lung	lung
8	chr2:95829600-95830800	Weak transcription	Left Ventricle	heart
9	chr2:95829600-95830800	Weak transcription	Pancreas	Pancrea
10	chr2:95829800-95830800	Weak transcription	Spleen	Spleen
11	chr2:95829800-95830800	Flanking Active TSS	Dnd41	blood
12	chr2:95829800-95832400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:95829800-95832600	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:95830000-95830800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:95830000-95830800	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr2:95830000-95831000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:95830000-95831000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr2:95830000-95831600	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr2:95830000-95832000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr2:95830000-95832000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr2:95830000-95832000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:95830200-95830800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:95830200-95830800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr2:95830200-95830800	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr2:95830200-95830800	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr2:95830200-95830800	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr2:95830200-95830800	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr2:95830200-95830800	Flanking Active TSS	Osteobl	bone
29	chr2:95830200-95831000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:95830200-95831000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr2:95830200-95831000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:95830200-95831000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:95830200-95831000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr2:95830200-95831400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:95830200-95831800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr2:95830200-95832000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:95830200-95832000	Active TSS	Psoas Muscle	Psoas
38	chr2:95830200-95832000	Active TSS	Stomach Mucosa	stomach
39	chr2:95830200-95832000	Active TSS	HMEC	breast
40	chr2:95830200-95832000	Active TSS	K562	blood
41	chr2:95830200-95832000	Active TSS	NHLF	lung
42	chr2:95830200-95832200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr2:95830200-95832400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr2:95830200-95832600	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr2:95830400-95830800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:95830400-95830800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr2:95830400-95830800	Enhancers	Primary B cells from peripheral blood	blood
48	chr2:95830400-95830800	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr2:95830400-95830800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr2:95830400-95830800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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