Variant report

Variant	rs35037868
Chromosome Location	chr6:27759115-27759116
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27739695..27740963-chr6:27759065..27761089,16	K562	blood:
2	chr6:27753086..27755536-chr6:27756533..27760305,3	MCF-7	breast:
3	chr6:27485668..27488646-chr6:27758590..27761132,3	K562	blood:
4	chr6:27154579..27158488-chr6:27757538..27761648,4	MCF-7	breast:
5	chr6:27114006..27117036-chr6:27757765..27761399,4	MCF-7	breast:
6	chr6:27435057..27436916-chr6:27758569..27760207,2	K562	blood:
7	chr6:27744761..27747867-chr6:27758538..27761675,3	MCF-7	breast:
8	chr6:27109661..27117801-chr6:27755492..27760111,8	K562	blood:
9	chr6:27144331..27145885-chr6:27758916..27760697,2	MCF-7	breast:
10	chr6:27154554..27158026-chr6:27757603..27761465,4	K562	blood:
11	chr6:27486617..27489499-chr6:27758856..27760750,2	K562	blood:
12	chr6:27516838..27518363-chr6:27758772..27760622,2	K562	blood:
13	chr6:27124582..27127541-chr6:27758021..27760797,2	K562	blood:
14	chr6:27113525..27116337-chr6:27757197..27759712,2	MCF-7	breast:
15	chr6:27112343..27120362-chr6:27757252..27765476,17	K562	blood:
16	chr6:27519736..27522304-chr6:27757079..27759597,2	MCF-7	breast:
17	chr6:27738620..27740539-chr6:27758419..27760190,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10484399	0.81[EUR][1000 genomes]
rs13192965	0.94[EUR][1000 genomes]
rs13193480	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13193542	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13194781	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13195728	0.92[EUR][1000 genomes]
rs13199649	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13199772	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13199906	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13202291	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13202295	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13202775	0.87[EUR][1000 genomes]
rs13210634	0.94[EUR][1000 genomes]
rs13212318	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs13212651	0.89[EUR][1000 genomes]
rs13215275	0.94[EUR][1000 genomes]
rs13216117	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13217620	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13218875	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17693963	0.82[EUR][1000 genomes]
rs17695758	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17749927	0.94[EUR][1000 genomes]
rs17750747	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17751184	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17763089	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs200481	0.83[EUR][1000 genomes]
rs200482	0.81[EUR][1000 genomes]
rs200483	0.83[EUR][1000 genomes]
rs200485	0.83[EUR][1000 genomes]
rs200489	0.83[EUR][1000 genomes]
rs200490	0.81[EUR][1000 genomes]
rs200497	0.81[EUR][1000 genomes]
rs200501	0.83[EUR][1000 genomes]
rs2747054	0.83[EUR][1000 genomes]
rs28360499	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34064842	0.96[EUR][1000 genomes]
rs34105070	0.87[EUR][1000 genomes]
rs34194357	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34409918	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34432857	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34706883	0.92[EUR][1000 genomes]
rs34718920	0.92[EUR][1000 genomes]
rs34788973	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35202262	1.00[AFR][1000 genomes]
rs35339855	1.00[AFR][1000 genomes]
rs35501037	1.00[EUR][1000 genomes]
rs35715914	0.94[EUR][1000 genomes]
rs35819751	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs36101351	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36116761	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs370155	0.81[EUR][1000 genomes]
rs390764	0.83[EUR][1000 genomes]
rs401754	0.83[EUR][1000 genomes]
rs425335	1.00[AFR][1000 genomes]
rs45509595	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56405707	0.94[EUR][1000 genomes]
rs61742093	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66868086	0.89[EUR][1000 genomes]
rs67040724	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67101035	0.92[EUR][1000 genomes]
rs67652222	0.92[EUR][1000 genomes]
rs71537572	0.80[AMR][1000 genomes]
rs71559038	0.92[EUR][1000 genomes]
rs71559050	0.92[EUR][1000 genomes]
rs71559054	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72845046	0.92[EUR][1000 genomes]
rs72845070	0.94[EUR][1000 genomes]
rs72847313	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9368531	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35037868	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs35037868	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs35037868	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27751600-27759200	Weak transcription	Colonic Mucosa	Colon
2	chr6:27754000-27759200	Weak transcription	HepG2	liver
3	chr6:27755200-27759200	Weak transcription	K562	blood
4	chr6:27759000-27759200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
5	chr6:27759000-27759200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
6	chr6:27759000-27759200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
7	chr6:27759000-27759200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr6:27759000-27759200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:27759000-27759200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:27759000-27759200	Active TSS	Adipose Nuclei	Adipose
11	chr6:27759000-27759200	Enhancers	Fetal Intestine Large	intestine
12	chr6:27759000-27759200	Enhancers	Placenta	Placenta
13	chr6:27759000-27759200	Enhancers	Psoas Muscle	Psoas
14	chr6:27759000-27759200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:27759000-27759200	Enhancers	Rectal Smooth Muscle	rectum
16	chr6:27759000-27759200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
17	chr6:27759000-27759200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
18	chr6:27759000-27759400	Bivalent Enhancer	Primary T cells from cord blood	blood
19	chr6:27759000-27759400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:27759000-27759400	Active TSS	Brain Anterior Caudate	brain
21	chr6:27759000-27759400	Enhancers	Fetal Brain Male	brain
22	chr6:27759000-27759400	Active TSS	Fetal Lung	lung
23	chr6:27759000-27759400	Bivalent Enhancer	Fetal Thymus	thymus
24	chr6:27759000-27759400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr6:27759000-27759400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
26	chr6:27759000-27759600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr6:27759000-27759600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
28	chr6:27759000-27759600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:27759000-27759600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:27759000-27759600	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr6:27759000-27759800	Active TSS	Brain Germinal Matrix	brain
32	chr6:27759000-27760000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:27759000-27760200	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr6:27759000-27760200	Active TSS	Hela-S3	cervix
35	chr6:27759000-27760400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr6:27759000-27760400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:27759000-27760400	Active TSS	Brain Angular Gyrus	brain
38	chr6:27759000-27760400	Active TSS	Brain Cingulate Gyrus	brain
39	chr6:27759000-27760400	Active TSS	HMEC	breast
40	chr6:27759000-27760400	Active TSS	NH-A	brain
41	chr6:27759000-27760600	Active TSS	Ovary	ovary
42	chr6:27759000-27760600	Active TSS	Right Atrium	heart
43	chr6:27759000-27760600	Active TSS	Stomach Mucosa	stomach
44	chr6:27759000-27760800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:27759000-27760800	Active TSS	NHLF	lung
46	chr6:27759000-27761000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:27759000-27761000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:27759000-27761000	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr6:27759000-27761000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:27759000-27761000	Active TSS	Fetal Kidney	kidney

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