Variant report

Variant	rs1793
Chromosome Location	chr6:86308868-86308869
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:86308629-86311414	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:86308789-86309495	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:86308539-86309600	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:86308552-86311264	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr6:86308592-86308970	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:86308168-86309164	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr6:86302683-86324770	K562	blood:	n/a	n/a
8	IRF1	chr6:86308726-86308873	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:86308091..86310509-chr6:86386844..86389781,5	K562	blood:
2	chr6:86306147..86310004-chr6:86351299..86354372,3	MCF-7	breast:
3	chr6:86307661..86310525-chr6:86316183..86318206,2	MCF-7	breast:
4	chr6:86300286..86310605-chr6:86384413..86390498,39	K562	blood:
5	chr6:86308147..86310058-chr6:86348388..86350658,2	K562	blood:
6	chr6:86307722..86311863-chr6:86387029..86388748,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX14-3	chr6:86307939-86309022	NONHSAT113844

No data

Variant related genes	Relation type
SNX14	TF binding region
ENSG00000135316	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13192070	0.82[ASN][1000 genomes]
rs13194512	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13198956	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13202606	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13208740	1.00[CEU][hapmap]
rs16876230	0.84[EUR][1000 genomes]
rs16876340	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16876385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34239697	0.91[EUR][1000 genomes]
rs34898046	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34936540	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35121980	0.87[EUR][1000 genomes]
rs35367106	0.91[EUR][1000 genomes]
rs35694036	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35712823	0.87[EUR][1000 genomes]
rs35988746	0.83[EUR][1000 genomes]
rs36088473	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3734442	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[EUR][1000 genomes]
rs3900740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4707213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707220	0.80[CHB][hapmap]
rs55648312	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55810446	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67493405	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6906121	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6909402	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6909654	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6910641	0.85[EUR][1000 genomes]
rs6915519	0.96[EUR][1000 genomes]
rs71570763	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71570764	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71570766	0.91[EUR][1000 genomes]
rs7738371	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7740830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742792	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7766863	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7771577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450302	0.89[YRI][hapmap]

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

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86304400-86309200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:86304400-86319600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:86304400-86321000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:86304400-86321200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:86304400-86324200	Weak transcription	Ovary	ovary
6	chr6:86304400-86324200	Weak transcription	Small Intestine	intestine
7	chr6:86304400-86324400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:86304400-86324400	Weak transcription	Lung	lung
9	chr6:86304400-86329400	Weak transcription	Esophagus	oesophagus
10	chr6:86304600-86313600	Weak transcription	Placenta	Placenta
11	chr6:86304600-86314200	Weak transcription	Dnd41	blood
12	chr6:86304600-86314600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:86304600-86315000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:86304600-86315600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:86304600-86317000	Weak transcription	Primary T cells from cord blood	blood
16	chr6:86304600-86317200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:86304600-86317600	Weak transcription	Left Ventricle	heart
18	chr6:86304600-86318600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:86304600-86318800	Weak transcription	Fetal Brain Female	brain
20	chr6:86304600-86318800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:86304600-86319000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:86304600-86320200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:86304600-86320200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:86304600-86320400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:86304600-86321400	Weak transcription	Colonic Mucosa	Colon
26	chr6:86304600-86321600	Weak transcription	Thymus	Thymus
27	chr6:86304600-86323400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:86304600-86323400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:86304600-86324200	Weak transcription	Fetal Stomach	stomach
30	chr6:86304600-86331400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:86304800-86309200	Weak transcription	Fetal Intestine Small	intestine
32	chr6:86304800-86313400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:86304800-86315600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:86304800-86316200	Weak transcription	Primary B cells from cord blood	blood
35	chr6:86304800-86316200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:86304800-86316200	Weak transcription	HSMMtube	muscle
37	chr6:86304800-86316400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:86304800-86317000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:86304800-86317200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:86304800-86318400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:86304800-86319200	Weak transcription	Adipose Nuclei	Adipose
42	chr6:86304800-86319400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:86304800-86319600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:86304800-86320000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:86304800-86320200	Weak transcription	Colon Smooth Muscle	Colon
46	chr6:86304800-86320800	Weak transcription	Brain Anterior Caudate	brain
47	chr6:86304800-86321000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:86304800-86321000	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:86304800-86321200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:86304800-86324400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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