Variant report

Variant	rs6479499
Chromosome Location	chr9:96405864-96405865
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96405435..96406996-chr9:96417472..96420268,2	MCF-7	breast:
2	chr9:96405323..96407093-chr9:96410616..96412899,2	K562	blood:
3	chr9:96405323..96407583-chr9:96410616..96412899,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10761245	0.83[CHB][hapmap]
rs10761247	0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs10761251	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761252	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761254	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761255	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10992836	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992841	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11534279	0.83[CHB][hapmap]
rs11793637	0.82[CHB][hapmap]
rs12002044	0.83[CHB][hapmap]
rs1806458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2001589	0.83[CHB][hapmap]
rs2001994	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2398851	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398853	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398855	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs2398856	0.83[CHB][hapmap]
rs2398861	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3750354	0.83[CHB][hapmap]
rs3750358	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763605	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743930	0.88[ASN][1000 genomes]
rs4743931	0.89[CHB][hapmap]
rs4744264	0.83[ASN][1000 genomes]
rs6479500	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479501	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019745	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7024028	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7028306	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7849752	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs7868191	0.82[CHB][hapmap]

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	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96380200-96411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
3	chr9:96387000-96411800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:96392200-96412000	Weak transcription	HMEC	breast
5	chr9:96392200-96423600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:96393600-96406600	Weak transcription	GM12878-XiMat	blood
7	chr9:96396400-96412000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:96397200-96407800	Weak transcription	NHEK	skin
9	chr9:96398200-96411200	Weak transcription	HUVEC	blood vessel
10	chr9:96398200-96413800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:96399000-96423400	Strong transcription	Fetal Intestine Large	intestine
12	chr9:96399200-96406200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:96399400-96423600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:96400200-96412000	Weak transcription	Hela-S3	cervix
15	chr9:96400400-96406800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:96400400-96407200	Weak transcription	Brain Substantia Nigra	brain
17	chr9:96400400-96407200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:96400400-96412000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:96400400-96412000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:96400400-96430600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr9:96400600-96407600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:96400600-96411600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:96400600-96411800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:96400600-96412000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr9:96400800-96407600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:96400800-96411800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:96400800-96411800	Weak transcription	Fetal Brain Male	brain
28	chr9:96400800-96411800	Weak transcription	K562	blood
29	chr9:96401000-96409000	Weak transcription	Primary B cells from cord blood	blood
30	chr9:96401000-96411800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr9:96401000-96411800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:96401000-96411800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:96401000-96411800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:96401000-96412000	Weak transcription	A549	lung
35	chr9:96401000-96430000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:96401000-96438600	Weak transcription	Psoas Muscle	Psoas
37	chr9:96401400-96406200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:96401400-96406800	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:96401600-96423400	Strong transcription	Adipose Nuclei	Adipose
40	chr9:96401800-96411800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:96401800-96423400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:96402200-96406000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:96402200-96411600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:96402400-96406800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:96402400-96411800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:96402400-96411800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr9:96402600-96406800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:96402600-96407600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr9:96402600-96430200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:96402600-96433600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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