Variant report

Variant	rs10484399
Chromosome Location	chr6:27534528-27534529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27514757..27519080-chr6:27534326..27537789,3	K562	blood:
2	chr6:27524177..27527153-chr6:27531672..27535728,3	MCF-7	breast:
3	chr6:27532784..27536184-chr6:27537874..27540243,4	K562	blood:
4	chr6:27518662..27523972-chr6:27530343..27535715,8	K562	blood:
5	chr6:27529191..27531638-chr6:27533093..27535191,2	K562	blood:
6	chr6:27532973..27535068-chr6:27541165..27542724,2	K562	blood:
7	chr6:27532266..27536184-chr6:27537870..27540243,4	K562	blood:
8	chr6:27528306..27529946-chr6:27532620..27534637,2	MCF-7	breast:
9	chr6:27532623..27535233-chr6:27560375..27562747,2	K562	blood:
10	chr6:27531650..27535233-chr6:27560375..27562860,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000219738	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs13191227	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13191474	0.89[EUR][1000 genomes]
rs13192965	0.87[EUR][1000 genomes]
rs13193480	0.81[EUR][1000 genomes]
rs13193542	0.81[EUR][1000 genomes]
rs13195040	0.90[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs13195636	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13196692	0.81[EUR][1000 genomes]
rs13202295	0.81[EUR][1000 genomes]
rs13202775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13207689	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13209332	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13210634	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs13212318	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13215275	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs13217620	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13218537	0.81[EUR][1000 genomes]
rs17693963	1.00[CEU][hapmap]
rs17749927	0.87[EUR][1000 genomes]
rs17750747	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs34064842	0.85[EUR][1000 genomes]
rs34105070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34196306	0.88[EUR][1000 genomes]
rs34332556	0.81[EUR][1000 genomes]
rs34409918	0.85[EUR][1000 genomes]
rs34432857	0.85[EUR][1000 genomes]
rs34573979	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34613987	0.87[EUR][1000 genomes]
rs34864796	0.87[EUR][1000 genomes]
rs34953377	0.81[EUR][1000 genomes]
rs34965299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35037868	0.81[EUR][1000 genomes]
rs35120058	0.81[EUR][1000 genomes]
rs35501037	0.81[EUR][1000 genomes]
rs35715914	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35848276	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41269265	0.89[EUR][1000 genomes]
rs56405707	0.87[EUR][1000 genomes]
rs58616630	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs66785117	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66841633	0.81[EUR][1000 genomes]
rs67240003	0.87[EUR][1000 genomes]
rs67652222	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67859638	0.83[EUR][1000 genomes]
rs6904596	0.87[EUR][1000 genomes]
rs6918792	0.86[EUR][1000 genomes]
rs71559038	0.85[EUR][1000 genomes]
rs72845046	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72845070	0.87[EUR][1000 genomes]
rs72847313	0.81[EUR][1000 genomes]
rs7749305	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10484399	BTN3A2	cis	multi-tissue	Pritchard
rs10484399	BTN3A2	trans	lymphoblastoid	seeQTL
rs10484399	HLA-A	cis	multi-tissue	Pritchard
rs10484399	LOC100270746	cis	lymphoblastoid	seeQTL
rs10484399	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs10484399	HLA-H	cis	multi-tissue	Pritchard
rs10484399	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs10484399	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27532000-27535800	Weak transcription	K562	blood
2	chr6:27533200-27534800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:27533200-27534800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:27533400-27534600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27533400-27534600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:27533400-27534600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:27533400-27534800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:27533400-27534800	Active TSS	A549	lung
9	chr6:27533600-27534600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr6:27533600-27534800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:27533600-27534800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:27533600-27534800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27533600-27535000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:27533800-27534800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:27533800-27535000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:27534200-27534600	Active TSS	GM12878-XiMat	blood
17	chr6:27534200-27534600	Bivalent/Poised TSS	NHEK	skin
18	chr6:27534400-27534600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:27534400-27534600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:27534400-27534600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:27534400-27534600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:27534400-27534800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:27534400-27535600	Weak transcription	HMEC	breast
24	chr6:27534400-27536200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:27534400-27536600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:27534400-27537000	Bivalent Enhancer	Placenta	Placenta

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