Variant report

Variant	rs6499268
Chromosome Location	chr16:69906529-69906530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69906020..69907607-chr16:69913429..69915841,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10852460	0.87[ASN][1000 genomes]
rs10852461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075742	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11075744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1116544	0.90[ASN][1000 genomes]
rs11642008	0.94[ASN][1000 genomes]
rs11648348	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12446168	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12446197	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12598642	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12919094	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12921407	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12926791	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12927052	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12927431	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1437134	0.81[CEU][hapmap]
rs1466863	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1500337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1566454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566455	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1566456	0.90[ASN][1000 genomes]
rs2102067	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2133799	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2291959	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2362641	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2362642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2937121	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3790075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790078	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3790080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790082	0.94[ASN][1000 genomes]
rs3790083	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4146819	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs4296254	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4985447	0.80[ASN][1000 genomes]
rs4985448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985450	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs55887947	0.90[ASN][1000 genomes]
rs6499244	0.85[CEU][hapmap]
rs6499263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499269	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68161338	0.81[EUR][1000 genomes]
rs7190013	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192213	0.88[EUR][1000 genomes]
rs7193038	0.92[EUR][1000 genomes]
rs7196842	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7200258	0.92[ASN][1000 genomes]
rs7202233	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs73572177	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7359336	0.81[CEU][hapmap]
rs8044876	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8047194	0.90[ASN][1000 genomes]
rs8047682	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8048550	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8049373	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8050414	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8050516	0.94[ASN][1000 genomes]
rs8051168	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8052225	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8060478	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8063226	0.94[ASN][1000 genomes]
rs9927967	0.92[ASN][1000 genomes]
rs9936589	0.87[ASN][1000 genomes]
rs9936723	0.87[ASN][1000 genomes]
rs9940315	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv960355	chr16:69901844-69907446	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6499268	LOC283970	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69890400-69923400	Weak transcription	HUVEC	blood vessel
3	chr16:69893000-69906800	Weak transcription	GM12878-XiMat	blood
4	chr16:69893000-69907000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr16:69893000-69934800	Weak transcription	Hela-S3	cervix
6	chr16:69893200-69923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:69893600-69910600	Weak transcription	A549	lung
8	chr16:69895800-69907000	Weak transcription	Small Intestine	intestine
9	chr16:69896000-69909400	Weak transcription	Fetal Kidney	kidney
10	chr16:69896400-69906600	Weak transcription	Stomach Mucosa	stomach
11	chr16:69896400-69910000	Weak transcription	Fetal Lung	lung
12	chr16:69896600-69906600	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:69896600-69909200	Strong transcription	Fetal Intestine Small	intestine
14	chr16:69896600-69910200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr16:69896800-69907200	Weak transcription	Right Atrium	heart
16	chr16:69900000-69914600	Weak transcription	NHLF	lung
17	chr16:69900200-69910000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr16:69900200-69914600	Weak transcription	NH-A	brain
19	chr16:69900800-69915600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr16:69900800-69933400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr16:69901000-69910000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr16:69901000-69910600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr16:69901000-69910600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr16:69901000-69912600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr16:69901000-69915200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr16:69901000-69915200	Strong transcription	Primary T cells from cord blood	blood
27	chr16:69901000-69918800	Strong transcription	Fetal Intestine Large	intestine
28	chr16:69901200-69909600	Strong transcription	Primary B cells from cord blood	blood
29	chr16:69901200-69910200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr16:69901800-69907400	Weak transcription	K562	blood
31	chr16:69901800-69922000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr16:69901800-69924600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr16:69902000-69910800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr16:69902000-69912400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr16:69902200-69906600	Weak transcription	Osteobl	bone
36	chr16:69902600-69914400	Weak transcription	HSMM	muscle
37	chr16:69902600-69924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr16:69902800-69906600	Weak transcription	HSMMtube	muscle
39	chr16:69902800-69910800	Weak transcription	Fetal Heart	heart
40	chr16:69903200-69912800	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr16:69903600-69910200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr16:69903800-69909800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr16:69903800-69917600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr16:69904200-69951200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr16:69904400-69908400	Strong transcription	Spleen	Spleen
46	chr16:69904400-69909000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr16:69904400-69910400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr16:69904400-69911600	Strong transcription	Fetal Thymus	thymus
49	chr16:69904400-69911800	Strong transcription	Thymus	Thymus
50	chr16:69904600-69910600	Strong transcription	Rectal Mucosa Donor 29	rectum

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