Variant report

Variant	rs2451716
Chromosome Location	chr6:26655594-26655595
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26643127..26645242-chr6:26653375..26655691,2	K562	blood:
2	chr6:26653678..26657411-chr6:26657507..26660873,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181315	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs2451714	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451717	0.82[ASN][1000 genomes]
rs2451739	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2451742	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2451746	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451749	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2451752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494691	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494706	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494710	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494714	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2494715	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2498342	0.90[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2498343	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3807029	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4591839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902411	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6915555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6919391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6929908	0.84[JPT][hapmap]
rs6931849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379892	0.84[JPT][hapmap]
rs9379902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379903	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2451716	RP11-457M11.2	cis	Thyroid	GTEx
rs2451716	ZNF322	cis	Adipose Subcutaneous	GTEx
rs2451716	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2451716	ZNF322	cis	Nerve Tibial	GTEx
rs2451716	ZNF322	cis	Thyroid	GTEx
rs2451716	RP11-457M11.2	cis	lung	GTEx
rs2451716	RP11-457M11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2451716	RP11-457M11.2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26633000-26658000	Weak transcription	Fetal Brain Male	brain
2	chr6:26641400-26659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:26641400-26659000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:26643400-26657600	Weak transcription	Right Ventricle	heart
5	chr6:26643400-26658800	Weak transcription	Pancreas	Pancrea
6	chr6:26643400-26659000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:26643400-26659000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:26643400-26659000	Weak transcription	Aorta	Aorta
9	chr6:26643400-26659000	Weak transcription	Lung	lung
10	chr6:26643400-26659400	Weak transcription	Esophagus	oesophagus
11	chr6:26643400-26659400	Weak transcription	Gastric	stomach
12	chr6:26643600-26655600	Weak transcription	Left Ventricle	heart
13	chr6:26643600-26657600	Weak transcription	Psoas Muscle	Psoas
14	chr6:26643600-26658000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:26643600-26658200	Weak transcription	Brain Germinal Matrix	brain
16	chr6:26643800-26657800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:26643800-26658400	Weak transcription	Fetal Heart	heart
18	chr6:26643800-26658400	Weak transcription	Small Intestine	intestine
19	chr6:26644000-26656000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:26644000-26657600	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:26644000-26657600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:26644000-26658000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:26644000-26658000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:26644000-26658200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:26644000-26658400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:26644000-26658400	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:26644200-26658000	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:26644600-26657600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:26644600-26658000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:26644600-26659000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:26644800-26657600	Weak transcription	Brain Angular Gyrus	brain
32	chr6:26644800-26658000	Weak transcription	Thymus	Thymus
33	chr6:26644800-26658000	Weak transcription	Hela-S3	cervix
34	chr6:26644800-26658400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:26644800-26658400	Weak transcription	HUVEC	blood vessel
36	chr6:26644800-26658400	Weak transcription	NH-A	brain
37	chr6:26645000-26658200	Weak transcription	NHLF	lung
38	chr6:26645000-26658600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:26645600-26658000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:26645600-26658400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:26645600-26658400	Weak transcription	HSMMtube	muscle
42	chr6:26646400-26658400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:26648000-26656800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr6:26648200-26656600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:26648600-26656200	Strong transcription	Fetal Lung	lung
46	chr6:26648800-26657200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:26648800-26658000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:26649000-26658000	Weak transcription	Brain Substantia Nigra	brain
49	chr6:26649200-26658400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:26649800-26659000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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