Variant report

Variant	rs17749927
Chromosome Location	chr6:27669976-27669977
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	chr6:27669358..27671049-chr6:27700076..27702911,2	K562	blood:
2	chr6:27663855..27666018-chr6:27668315..27670242,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10484399	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs13192965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193480	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13193542	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13194781	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13195636	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13195728	0.87[EUR][1000 genomes]
rs13199649	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13199772	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13199906	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13202291	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13202295	0.94[EUR][1000 genomes]
rs13202775	0.92[EUR][1000 genomes]
rs13209332	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs13210634	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13212318	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13212651	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13215275	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13217620	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs175597	0.91[CEU][hapmap]
rs17693963	1.00[CEU][hapmap]
rs17695758	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17750747	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17751184	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17763089	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs200481	0.91[CEU][hapmap]
rs200482	0.91[CEU][hapmap]
rs200483	0.91[CEU][hapmap]
rs200484	0.91[CEU][hapmap]
rs200485	0.91[CEU][hapmap]
rs200490	0.91[CEU][hapmap]
rs200501	0.91[CEU][hapmap]
rs200948	0.91[CEU][hapmap]
rs200949	0.91[CEU][hapmap]
rs200953	0.91[CEU][hapmap]
rs200954	0.91[CEU][hapmap]
rs200977	0.91[CEU][hapmap]
rs200981	0.89[CEU][hapmap]
rs200989	0.91[CEU][hapmap]
rs200990	0.91[CEU][hapmap]
rs200995	0.91[CEU][hapmap]
rs201002	0.91[CEU][hapmap]
rs2747054	0.91[CEU][hapmap]
rs34064842	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34105070	0.92[EUR][1000 genomes]
rs34194357	0.83[EUR][1000 genomes]
rs34409918	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34432857	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34573979	0.81[EUR][1000 genomes]
rs34706883	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs34718920	0.87[EUR][1000 genomes]
rs34788973	0.80[EUR][1000 genomes]
rs34965299	0.85[EUR][1000 genomes]
rs35037868	0.94[EUR][1000 genomes]
rs35501037	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35715914	1.00[EUR][1000 genomes]
rs35819751	0.83[EUR][1000 genomes]
rs35848276	0.85[EUR][1000 genomes]
rs36116761	0.83[EUR][1000 genomes]
rs370155	0.91[CEU][hapmap]
rs401763	0.91[CEU][hapmap]
rs425335	1.00[CEU][hapmap]
rs45509595	0.83[EUR][1000 genomes]
rs56405707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58616630	0.81[EUR][1000 genomes]
rs61742093	0.80[EUR][1000 genomes]
rs66785117	0.85[EUR][1000 genomes]
rs66868086	0.83[EUR][1000 genomes]
rs67101035	0.87[EUR][1000 genomes]
rs67652222	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs71559038	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71559050	0.87[EUR][1000 genomes]
rs72845046	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs72845070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847313	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv437481	chr6:27655096-27683572	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv601204	chr6:27655564-27689502	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1023808	chr6:27656049-27674354	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17749927	BTN3A2	trans	lymphoblastoid	seeQTL
rs17749927	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs17749927	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs17749927	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs17749927	LOC100270746	cis	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27662400-27678000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:27662400-27680000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:27662400-27680400	Weak transcription	Spleen	Spleen
4	chr6:27662400-27680600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:27662400-27684600	Weak transcription	Lung	lung
6	chr6:27662400-27685600	Weak transcription	Esophagus	oesophagus
7	chr6:27662600-27670000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:27662600-27670800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:27662600-27673200	Weak transcription	Fetal Stomach	stomach
10	chr6:27662600-27678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:27662600-27678600	Weak transcription	Primary B cells from cord blood	blood
12	chr6:27662600-27680600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:27662600-27680800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:27662600-27684000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:27662800-27670000	Weak transcription	Primary T cells from cord blood	blood
16	chr6:27662800-27670000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:27662800-27670000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:27662800-27670200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:27662800-27670800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:27662800-27671000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:27662800-27671200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:27662800-27672400	Weak transcription	Fetal Intestine Small	intestine
23	chr6:27662800-27678400	Weak transcription	Fetal Lung	lung
24	chr6:27662800-27678400	Weak transcription	Thymus	Thymus
25	chr6:27662800-27678600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:27662800-27684000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:27662800-27684800	Weak transcription	Fetal Kidney	kidney
28	chr6:27662800-27688400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:27662800-27688600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:27662800-27689000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:27663000-27670000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:27663000-27670800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:27663000-27674600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:27663000-27688600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:27663200-27670000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:27663200-27670000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:27663200-27670000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:27663200-27670000	Weak transcription	Fetal Intestine Large	intestine
39	chr6:27663200-27670000	Weak transcription	Ovary	ovary
40	chr6:27663200-27670200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:27663200-27670200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:27663200-27670800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:27663200-27670800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:27663200-27671200	Weak transcription	Fetal Thymus	thymus
45	chr6:27663200-27673000	Weak transcription	GM12878-XiMat	blood
46	chr6:27663200-27674200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:27663200-27676400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:27663200-27678200	Weak transcription	Brain Germinal Matrix	brain
49	chr6:27663200-27678200	Weak transcription	Fetal Brain Female	brain
50	chr6:27663200-27680800	Weak transcription	H9 Cell Line	embryonic stem cell

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