Variant report

Variant	rs6499257
Chromosome Location	chr16:69833663-69833664
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69833036..69834030-chr16:69971100..69971839,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11075734	0.83[LWK][hapmap];0.86[MKK][hapmap]
rs11075738	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11075739	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11641521	0.82[AFR][1000 genomes]
rs11641899	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11643817	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12447095	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12596679	0.81[ASW][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes]
rs2173714	0.88[ASN][1000 genomes]
rs34378064	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3790085	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs3790086	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4275849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4341733	1.00[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];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4464069	0.85[MKK][hapmap]
rs4985418	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985445	0.87[ASN][1000 genomes]
rs4985446	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985518	0.81[ASW][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap]
rs55863174	0.80[AFR][1000 genomes]
rs55992518	0.80[AFR][1000 genomes]
rs56282083	0.94[AFR][1000 genomes]
rs60231938	0.94[AFR][1000 genomes]
rs60941540	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62051384	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62051387	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62051389	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499260	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7193221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7194806	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7196917	0.88[CEU][hapmap]
rs7200005	0.88[CEU][hapmap]
rs7202223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7206585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73579497	0.94[AFR][1000 genomes]
rs8044920	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8045682	0.81[ASW][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap]
rs8052428	0.95[CEU][hapmap]
rs8057620	0.81[CHD][hapmap]
rs8059645	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8063219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9630631	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[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	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6499257	LOC440348	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69797600-69853400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:69807200-69852400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:69807200-69852800	Weak transcription	Hela-S3	cervix
4	chr16:69807200-69854800	Weak transcription	Psoas Muscle	Psoas
5	chr16:69810000-69839800	Weak transcription	HUVEC	blood vessel
6	chr16:69817800-69854600	Weak transcription	HMEC	breast
7	chr16:69820200-69845000	Weak transcription	K562	blood
8	chr16:69822400-69854800	Weak transcription	Stomach Mucosa	stomach
9	chr16:69823800-69874800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr16:69824200-69852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:69830000-69839000	Strong transcription	HepG2	liver
12	chr16:69830200-69856600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr16:69830600-69833800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr16:69830600-69838400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr16:69830600-69857600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:69830600-69864200	Weak transcription	Colon Smooth Muscle	Colon
17	chr16:69830600-69867000	Weak transcription	Right Ventricle	heart
18	chr16:69831000-69845000	Weak transcription	Fetal Brain Male	brain
19	chr16:69831000-69845600	Weak transcription	A549	lung
20	chr16:69831000-69852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr16:69831000-69852400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr16:69831000-69854800	Weak transcription	Aorta	Aorta
23	chr16:69831000-69856400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr16:69831200-69846200	Strong transcription	Fetal Intestine Small	intestine
25	chr16:69831600-69838800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr16:69832000-69834200	Strong transcription	Primary B cells from cord blood	blood
27	chr16:69832000-69834400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr16:69832000-69834800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr16:69832000-69836800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr16:69832000-69837800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr16:69832000-69838800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr16:69832400-69833800	Enhancers	Osteobl	bone
33	chr16:69832400-69834000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr16:69832400-69834200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:69832400-69834200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr16:69832400-69835200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr16:69832400-69835600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr16:69832400-69837000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr16:69832400-69858400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr16:69832600-69833800	Strong transcription	Esophagus	oesophagus
41	chr16:69832600-69833800	Strong transcription	Fetal Thymus	thymus
42	chr16:69832600-69833800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
43	chr16:69832600-69833800	Strong transcription	NHEK	skin
44	chr16:69832600-69834000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:69832600-69834000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:69832600-69834000	Strong transcription	Fetal Brain Female	brain
47	chr16:69832600-69834000	Strong transcription	Gastric	stomach
48	chr16:69832600-69834200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr16:69832600-69834200	Strong transcription	Placenta	Placenta
50	chr16:69832600-69834200	Strong transcription	Rectal Mucosa Donor 29	rectum

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