Variant report

Variant	rs13207689
Chromosome Location	chr6:27369704-27369705
allele	C/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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27360610..27362921-chr6:27368248..27371052,2	MCF-7	breast:
2	chr6:27363554..27367371-chr6:27369337..27372451,5	K562	blood:
3	chr6:27355079..27357819-chr6:27369323..27370983,2	K562	blood:
4	chr6:27276042..27278512-chr6:27366738..27369712,2	K562	blood:
5	chr6:27368618..27370867-chr6:27411111..27412908,2	K562	blood:
6	chr6:27363318..27368170-chr6:27368582..27372451,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRSS16-5	chr6:27369662-27371681	NONHSAT108382

No data

Variant related genes	Relation type
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484399	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13191227	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13191474	0.91[EUR][1000 genomes]
rs13195040	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs13195636	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13196692	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13209332	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13212562	0.82[EUR][1000 genomes]
rs13218537	0.98[EUR][1000 genomes]
rs28360634	0.96[EUR][1000 genomes]
rs34071253	0.96[EUR][1000 genomes]
rs34196306	0.90[EUR][1000 genomes]
rs34332556	0.98[EUR][1000 genomes]
rs34573979	0.89[EUR][1000 genomes]
rs34613987	0.82[EUR][1000 genomes]
rs34864796	0.82[EUR][1000 genomes]
rs34953377	0.98[EUR][1000 genomes]
rs34965299	0.85[EUR][1000 genomes]
rs35120058	0.98[EUR][1000 genomes]
rs35716472	0.96[EUR][1000 genomes]
rs35848276	0.85[EUR][1000 genomes]
rs35984974	0.96[EUR][1000 genomes]
rs41269265	0.91[EUR][1000 genomes]
rs56401801	0.90[EUR][1000 genomes]
rs58616630	0.89[EUR][1000 genomes]
rs66785117	0.85[EUR][1000 genomes]
rs66841633	0.98[EUR][1000 genomes]
rs67240003	0.82[EUR][1000 genomes]
rs67859638	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6904596	0.82[EUR][1000 genomes]
rs6918792	0.81[EUR][1000 genomes]
rs71537559	0.92[EUR][1000 genomes]
rs72839477	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7749305	1.00[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1031803	chr6:27355881-27423655	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv538166	chr6:27355881-27423655	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv5235	chr6:27358498-27404074	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13207689	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs13207689	BTN3A2	cis	uninvolved skin	skin_eQTL
rs13207689	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs13207689	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27359600-27371200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:27359600-27372200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:27360000-27371400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr6:27360600-27370800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:27363000-27372200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:27364000-27370800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:27364800-27369800	ZNF genes & repeats	Fetal Muscle Leg	muscle
8	chr6:27364800-27370600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr6:27365000-27370000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr6:27365000-27370400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
11	chr6:27365000-27370400	ZNF genes & repeats	Fetal Lung	lung
12	chr6:27365800-27370800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
13	chr6:27366000-27370200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr6:27366600-27370600	ZNF genes & repeats	Ovary	ovary
15	chr6:27366800-27369800	ZNF genes & repeats	Aorta	Aorta
16	chr6:27366800-27369800	ZNF genes & repeats	Fetal Brain Female	brain
17	chr6:27366800-27369800	ZNF genes & repeats	Dnd41	blood
18	chr6:27367000-27370000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:27367000-27370000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr6:27367000-27370000	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr6:27367000-27370400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr6:27367200-27369800	ZNF genes & repeats	Colon Smooth Muscle	Colon
23	chr6:27367400-27370200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
24	chr6:27367400-27372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:27367800-27369800	ZNF genes & repeats	Brain Hippocampus Middle	brain
26	chr6:27367800-27369800	ZNF genes & repeats	Left Ventricle	heart
27	chr6:27367800-27369800	ZNF genes & repeats	Psoas Muscle	Psoas
28	chr6:27367800-27371200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:27368400-27369800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:27368800-27369800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27368800-27370400	Weak transcription	Fetal Heart	heart
32	chr6:27369000-27369800	Strong transcription	Brain Germinal Matrix	brain
33	chr6:27369000-27370800	Weak transcription	Fetal Kidney	kidney
34	chr6:27369000-27376600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:27369200-27371000	Weak transcription	Brain Anterior Caudate	brain
36	chr6:27369200-27372600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:27369200-27382000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:27369400-27369800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:27369600-27370600	ZNF genes & repeats	Fetal Stomach	stomach
40	chr6:27369600-27372600	Weak transcription	Fetal Brain Male	brain
41	chr6:27369600-27374200	Weak transcription	Fetal Muscle Trunk	muscle

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