Variant report

Variant	rs2494705
Chromosome Location	chr6:26641172-26641173
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	SPI1	chr6:26641014-26641442	HL-60	blood:	n/a	chr6:26641235-26641244 chr6:26641232-26641245

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
ENSG00000233631	TF binding region
ENSG00000181315	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2451714	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451715	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451716	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]
rs2451717	0.80[ASN][1000 genomes]
rs2451739	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2451742	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451746	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]
rs2451749	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451753	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451754	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494691	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2494706	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494708	0.81[ASN][1000 genomes]
rs2494710	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494711	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494714	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2494715	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2498342	0.95[CHB][hapmap];0.92[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2498343	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800302	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3807029	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4591839	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6902411	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6915555	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6919391	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929908	0.84[JPT][hapmap]
rs6931849	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7765920	0.85[MKK][hapmap]
rs9379892	0.84[JPT][hapmap]
rs9379902	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9379903	0.84[AFR][1000 genomes];0.92[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2494705	ZNF322B	trans	multi-tissue	Pritchard
rs2494705	ZNF204P	cis	cerebellum	SCAN
rs2494705	RP11-457M11.2	cis	lung	GTEx
rs2494705	BTN2A2	cis	cerebellum	SCAN
rs2494705	RP11-457M11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2494705	HIST1H4L	cis	parietal	SCAN
rs2494705	RP11-457M11.2	cis	Thyroid	GTEx
rs2494705	BTN3A2	cis	cerebellum	SCAN
rs2494705	BTN3A2	cis	parietal	SCAN
rs2494705	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2494705	ZNF322	cis	Thyroid	GTEx
rs2494705	ZNF322	cis	Nerve Tibial	GTEx
rs2494705	ZNF322	cis	Artery Tibial	GTEx
rs2494705	ZNF322	cis	Adipose Subcutaneous	GTEx
rs2494705	HIST1H3E	cis	cerebellum	SCAN
rs2494705	RP11-457M11.2	cis	Artery Tibial	GTEx
rs2494705	BTN3A3	cis	cerebellum	SCAN

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	chr6:26636400-26645800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:26636800-26645800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr6:26637600-26645800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:26638000-26645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:26638200-26641800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:26638400-26643600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:26638400-26644800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:26638400-26646800	ZNF genes & repeats	Liver	Liver
10	chr6:26638800-26641400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
11	chr6:26638800-26641400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr6:26638800-26641600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr6:26638800-26641600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:26638800-26641800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:26638800-26642600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr6:26638800-26644400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
17	chr6:26638800-26644800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:26638800-26645400	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr6:26638800-26645600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:26638800-26646600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:26638800-26646800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:26638800-26646800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:26639000-26641200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
24	chr6:26639000-26641200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr6:26639000-26641200	ZNF genes & repeats	NH-A	brain
26	chr6:26639000-26641400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:26639000-26641400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
28	chr6:26639000-26641400	ZNF genes & repeats	Fetal Intestine Large	intestine
29	chr6:26639000-26641400	ZNF genes & repeats	HepG2	liver
30	chr6:26639000-26641800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr6:26639000-26641800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:26639000-26641800	ZNF genes & repeats	A549	lung
33	chr6:26639000-26642200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr6:26639000-26643400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:26639000-26643800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:26639000-26644200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:26639000-26644200	ZNF genes & repeats	NHEK	skin
38	chr6:26639000-26644600	Strong transcription	Placenta	Placenta
39	chr6:26639000-26644600	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr6:26639000-26644800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
41	chr6:26639000-26644800	Strong transcription	Dnd41	blood
42	chr6:26639000-26645000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr6:26639000-26645000	ZNF genes & repeats	HMEC	breast
44	chr6:26639000-26645200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
45	chr6:26639000-26645600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr6:26639000-26645600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:26639000-26645800	ZNF genes & repeats	GM12878-XiMat	blood
48	chr6:26639000-26646600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:26639000-26651800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:26639200-26641200	ZNF genes & repeats	Brain Hippocampus Middle	brain

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