Variant report

Variant	rs2451746
Chromosome Location	chr6:26640283-26640284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26639612..26641880-chr6:26658088..26660144,2	MCF-7	breast:
2	chr6:26640152..26642957-chr6:26643497..26647003,3	K562	blood:

Variant related genes	Relation type
ENSG00000181315	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2451714	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451715	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451716	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]
rs2451717	0.84[ASN][1000 genomes]
rs2451739	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2451742	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2451749	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2451752	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451753	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451754	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494705	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2494706	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2494708	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2494710	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2494711	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2494714	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2494715	0.87[ASN][1000 genomes]
rs2498342	0.84[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2498343	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800302	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3807029	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4591839	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902411	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6911540	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6915555	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6919391	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6929908	0.84[JPT][hapmap]
rs6931849	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379892	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9379902	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379903	0.87[EUR][1000 genomes];0.80[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2451746	RP11-457M11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2451746	RP11-457M11.2	cis	Adipose Subcutaneous	GTEx
rs2451746	ZNF322	cis	Nerve Tibial	GTEx
rs2451746	ZNF322	cis	Artery Tibial	GTEx
rs2451746	RP11-457M11.2	cis	Artery Tibial	GTEx
rs2451746	ZNF322	cis	Thyroid	GTEx
rs2451746	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2451746	RP11-457M11.2	cis	Thyroid	GTEx
rs2451746	RP11-457M11.2	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26631800-26640400	Weak transcription	Pancreas	Pancrea
2	chr6:26632000-26640600	Weak transcription	Fetal Stomach	stomach
3	chr6:26633000-26640400	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:26633000-26658000	Weak transcription	Fetal Brain Male	brain
5	chr6:26633400-26640600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:26636400-26645800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:26636800-26645800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr6:26637400-26640800	Weak transcription	Stomach Mucosa	stomach
9	chr6:26637600-26645800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:26638000-26640400	Weak transcription	Fetal Thymus	thymus
11	chr6:26638000-26645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:26638200-26641800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:26638400-26643600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:26638400-26644800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:26638400-26646800	ZNF genes & repeats	Liver	Liver
16	chr6:26638800-26641400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr6:26638800-26641400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr6:26638800-26641600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr6:26638800-26641600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:26638800-26641800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:26638800-26642600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr6:26638800-26644400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
23	chr6:26638800-26644800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:26638800-26645400	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr6:26638800-26645600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:26638800-26646600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:26638800-26646800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:26638800-26646800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:26639000-26640600	Strong transcription	Hela-S3	cervix
30	chr6:26639000-26640800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:26639000-26641000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:26639000-26641000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
33	chr6:26639000-26641000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
34	chr6:26639000-26641000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
35	chr6:26639000-26641200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
36	chr6:26639000-26641200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
37	chr6:26639000-26641200	ZNF genes & repeats	NH-A	brain
38	chr6:26639000-26641400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:26639000-26641400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr6:26639000-26641400	ZNF genes & repeats	Fetal Intestine Large	intestine
41	chr6:26639000-26641400	ZNF genes & repeats	HepG2	liver
42	chr6:26639000-26641800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr6:26639000-26641800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:26639000-26641800	ZNF genes & repeats	A549	lung
45	chr6:26639000-26642200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
46	chr6:26639000-26643400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:26639000-26643800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:26639000-26644200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:26639000-26644200	ZNF genes & repeats	NHEK	skin
50	chr6:26639000-26644600	Strong transcription	Placenta	Placenta

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