Variant report

Variant	rs897059
Chromosome Location	chr12:50202711-50202712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr12:50202298-50202982	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAZ	chr12:50202368-50203544	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:50202042..50204692-chr12:50235027..50237888,2	K562	blood:
2	chr12:50202054..50204119-chr12:50221111..50223703,2	K562	blood:
3	chr12:50200354..50203165-chr12:50213791..50216673,2	K562	blood:
4	chr12:50202445..50204111-chr12:50220708..50222560,2	MCF-7	breast:
5	chr12:50200446..50205468-chr12:50207348..50211696,6	MCF-7	breast:
6	chr12:50202257..50205352-chr12:50220114..50222671,5	MCF-7	breast:
7	chr12:50198514..50201197-chr12:50201542..50204471,2	MCF-7	breast:
8	chr12:50189974..50194712-chr12:50201594..50205995,4	K562	blood:
9	chr12:50201332..50204489-chr12:50235415..50238606,4	MCF-7	breast:
10	chr12:50197457..50199102-chr12:50202144..50204971,2	K562	blood:
11	chr12:50200354..50204251-chr12:50212561..50215291,3	K562	blood:
12	chr12:50200740..50202923-chr12:50213695..50216667,2	MCF-7	breast:

No data

Variant related genes	Relation type
NCKAP5L	TF binding region
ENSG00000258057	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11169153	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169154	1.00[CEU][hapmap];0.92[MEX][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11169155	0.86[AMR][1000 genomes]
rs11169156	0.85[AMR][1000 genomes]
rs11169160	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169172	1.00[CEU][hapmap];0.93[CHD][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs1470907	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1470908	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3741554	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741555	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813526	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4898531	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4898533	1.00[CEU][hapmap];0.92[AMR][1000 genomes]
rs59429669	0.89[AMR][1000 genomes]
rs7134749	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
3	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
4	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:50184400-50203200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:50187200-50203000	Strong transcription	Primary T cells from cord blood	blood
7	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:50189200-50214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:50190400-50203000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:50192200-50203200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr12:50192200-50203800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr12:50193800-50214600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:50195200-50218400	Weak transcription	K562	blood
14	chr12:50195800-50214400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:50196200-50204000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:50196800-50203600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:50197600-50205000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr12:50197600-50220400	Weak transcription	A549	lung
19	chr12:50198600-50203600	Weak transcription	GM12878-XiMat	blood
20	chr12:50199200-50203000	Weak transcription	Aorta	Aorta
21	chr12:50199400-50203000	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:50199400-50203000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:50199400-50203400	Weak transcription	HUVEC	blood vessel
24	chr12:50199400-50203600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:50199400-50218400	Weak transcription	HMEC	breast
26	chr12:50199600-50205600	Enhancers	Right Atrium	heart
27	chr12:50199600-50205800	Weak transcription	Primary B cells from cord blood	blood
28	chr12:50199600-50214600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:50199600-50214800	Weak transcription	Liver	Liver
30	chr12:50199800-50206200	Enhancers	Fetal Heart	heart
31	chr12:50200000-50209800	Weak transcription	Spleen	Spleen
32	chr12:50200000-50213800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:50200000-50214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:50200000-50214600	Weak transcription	Pancreas	Pancrea
35	chr12:50200000-50216800	Weak transcription	NHEK	skin
36	chr12:50200000-50219400	Weak transcription	Gastric	stomach
37	chr12:50200200-50214800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:50200400-50202800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:50200400-50202800	Weak transcription	NHDF-Ad	bronchial
40	chr12:50200400-50203000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:50200400-50205600	Enhancers	Left Ventricle	heart
42	chr12:50200400-50214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:50200400-50215000	Weak transcription	Dnd41	blood
44	chr12:50200600-50203000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:50200600-50209600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:50200800-50205600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:50201200-50202800	Genic enhancers	Fetal Stomach	stomach
48	chr12:50201200-50205600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:50201400-50203000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:50201600-50203200	Strong transcription	Thymus	Thymus

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