Variant report

Variant	rs6902638
Chromosome Location	chr6:86318599-86318600
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:86317763..86319413-chr6:86348369..86350869,2	K562	blood:
2	chr6:86318224..86320035-chr6:86336365..86338344,2	K562	blood:
3	chr6:86317811..86321272-chr6:86386885..86389356,5	K562	blood:
4	chr6:86302449..86304718-chr6:86318057..86320057,2	MCF-7	breast:
5	chr6:86316114..86321272-chr6:86386849..86391556,8	K562	blood:
6	chr6:86317225..86321756-chr6:86386301..86389684,6	MCF-7	breast:
7	chr6:86312962..86319312-chr6:86381507..86386179,8	K562	blood:
8	chr6:86301714..86305650-chr6:86315501..86320547,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12055597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12524836	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12528808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12662033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12664908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1570311	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1590279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2229524	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3812139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4327657	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4373339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4400191	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4458647	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4487548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59744370	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6902904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6906618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6910543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6923017	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930543	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73751215	0.81[ASN][1000 genomes]
rs7744309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7745560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7749600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752105	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7753022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7760309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7766284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7771187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7771366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7775788	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9344530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9344538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351063	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351066	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353321	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353323	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9359656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9362223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9362225	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9362226	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444353	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444356	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs9450289	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450295	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450299	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450304	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6902638	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs6902638	NT5E	cis	Thyroid	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86304400-86319600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:86304400-86321000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:86304400-86321200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:86304400-86324200	Weak transcription	Ovary	ovary
5	chr6:86304400-86324200	Weak transcription	Small Intestine	intestine
6	chr6:86304400-86324400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:86304400-86324400	Weak transcription	Lung	lung
8	chr6:86304400-86329400	Weak transcription	Esophagus	oesophagus
9	chr6:86304600-86318600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:86304600-86318800	Weak transcription	Fetal Brain Female	brain
11	chr6:86304600-86318800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:86304600-86319000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:86304600-86320200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:86304600-86320200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:86304600-86320400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:86304600-86321400	Weak transcription	Colonic Mucosa	Colon
17	chr6:86304600-86321600	Weak transcription	Thymus	Thymus
18	chr6:86304600-86323400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:86304600-86323400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:86304600-86324200	Weak transcription	Fetal Stomach	stomach
21	chr6:86304600-86331400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:86304800-86319200	Weak transcription	Adipose Nuclei	Adipose
23	chr6:86304800-86319400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:86304800-86319600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:86304800-86320000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:86304800-86320200	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:86304800-86320800	Weak transcription	Brain Anterior Caudate	brain
28	chr6:86304800-86321000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:86304800-86321000	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:86304800-86321200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:86304800-86324400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:86305000-86319600	Weak transcription	NHEK	skin
33	chr6:86305000-86320200	Weak transcription	Fetal Lung	lung
34	chr6:86305000-86320400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:86305000-86320600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:86305000-86320800	Weak transcription	HepG2	liver
37	chr6:86305800-86336200	Weak transcription	Fetal Heart	heart
38	chr6:86306200-86320200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:86306200-86321000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:86307600-86331000	Strong transcription	HSMM	muscle
41	chr6:86309600-86324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:86310600-86319200	Weak transcription	NHLF	lung
43	chr6:86311200-86323400	Weak transcription	Psoas Muscle	Psoas
44	chr6:86311600-86321000	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:86312600-86323400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:86312800-86329600	Weak transcription	Aorta	Aorta
47	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr6:86313600-86323000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:86313600-86338400	Strong transcription	GM12878-XiMat	blood
50	chr6:86313800-86321000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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