Variant report

Variant	rs2396441
Chromosome Location	chr6:45467765-45467766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45464191..45466468-chr6:45467404..45469996,2	K562	blood:
2	chr6:45465666..45468253-chr6:45472384..45474862,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16873437	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1934328	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711816	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6914610	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7750470	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs7754187	0.88[JPT][hapmap]
rs7756144	0.86[ASN][1000 genomes]
rs7771889	0.94[JPT][hapmap]
rs7773875	0.86[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2396441	HSP90AB1	cis	parietal	SCAN
rs2396441	POLR1C	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45448400-45472000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:45448800-45468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:45449000-45472600	Weak transcription	NHEK	skin
4	chr6:45452000-45472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:45454000-45471800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:45458000-45469800	Weak transcription	Hela-S3	cervix
7	chr6:45459400-45472600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:45460000-45468400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:45461200-45480000	Weak transcription	NHDF-Ad	bronchial
10	chr6:45462400-45472000	Weak transcription	NHLF	lung
11	chr6:45462600-45468000	Weak transcription	Osteobl	bone
12	chr6:45462800-45469800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:45463400-45471600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:45463800-45468200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:45464000-45471800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:45464200-45472600	Weak transcription	K562	blood
17	chr6:45464400-45472600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:45464600-45470600	Weak transcription	NH-A	brain
19	chr6:45464800-45479800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:45465000-45468000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:45465000-45468800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:45465000-45469000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:45465000-45479400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:45465000-45480000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:45465000-45521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:45465800-45480000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:45466000-45480200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:45466400-45483400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:45466600-45468600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:45466800-45468400	Weak transcription	Dnd41	blood
31	chr6:45466800-45472600	Weak transcription	Gastric	stomach
32	chr6:45466800-45488200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:45466800-45497200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:45467000-45467800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:45467000-45468400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:45467200-45468000	Weak transcription	HSMM	muscle
37	chr6:45467200-45468200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:45467200-45468200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:45467200-45468800	Weak transcription	Psoas Muscle	Psoas
40	chr6:45467200-45471000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:45467200-45471200	Weak transcription	Fetal Thymus	thymus
42	chr6:45467200-45471800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:45467200-45472600	Weak transcription	Fetal Lung	lung
44	chr6:45467200-45472600	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:45467200-45475400	Weak transcription	Small Intestine	intestine
46	chr6:45467200-45480000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr6:45467200-45487800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:45467400-45468400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:45467400-45471800	Weak transcription	HSMMtube	muscle
50	chr6:45467400-45472000	Weak transcription	Primary T cells from cord blood	blood

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