Variant report

Variant	rs852402
Chromosome Location	chr7:5717261-5717262
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:5708885..5710643-chr7:5716339..5719013,2	K562	blood:
2	chr7:5602905..5603944-chr7:5717247..5718273,6	MCF-7	breast:
3	chr7:5634585..5636582-chr7:5716195..5717760,2	K562	blood:
4	chr7:5602882..5603782-chr7:5717241..5717818,2	K562	blood:
5	chr7:5716923..5718931-chr7:5730393..5732059,2	MCF-7	breast:
6	chr7:5563906..5565672-chr7:5715265..5717638,2	K562	blood:
7	chr7:5567652..5570729-chr7:5716334..5720767,4	MCF-7	breast:
8	chr7:5603045..5605168-chr7:5716278..5719037,2	MCF-7	breast:
9	chr7:5561140..5562775-chr7:5716624..5718720,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000075624	Chromatin interaction
ENSG00000263900	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10232762	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233615	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10241310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259773	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10275238	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1035331	0.94[ASN][1000 genomes]
rs11531468	0.94[ASN][1000 genomes]
rs12531598	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1990836	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2009260	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287595	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs2345938	0.85[AFR][1000 genomes]
rs3735289	1.00[ASN][1000 genomes]
rs3801016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3801019	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807580	0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3823683	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4720641	0.92[ASN][1000 genomes]
rs4720642	0.92[ASN][1000 genomes]
rs4724712	1.00[CHB][hapmap]
rs4724713	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724718	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs61203027	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6463506	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463507	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944143	0.92[ASN][1000 genomes]
rs6956960	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958272	0.80[ASN][1000 genomes]
rs6959871	0.88[JPT][hapmap]
rs6960381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6960897	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6971289	0.88[MEX][hapmap]
rs710941	0.85[AMR][1000 genomes]
rs7777831	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795879	0.86[JPT][hapmap]
rs7796461	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800691	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803308	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7806110	0.88[JPT][hapmap];0.88[MEX][hapmap]
rs852257	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852258	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852265	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852266	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852267	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852375	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852376	0.81[ASW][hapmap];1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852396	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs852397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852409	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs852415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs852420	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852421	0.83[EUR][1000 genomes]
rs852438	0.86[YRI][hapmap]
rs852441	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs852442	0.83[YRI][hapmap]
rs852448	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs852450	0.85[AMR][1000 genomes]
rs852453	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs852457	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs852461	0.85[AMR][1000 genomes]
rs852468	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852472	0.85[AMR][1000 genomes]
rs852489	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes]
rs852516	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs860425	0.85[AMR][1000 genomes]
rs888582	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888583	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648578	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9691118	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
5	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
6	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
7	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
8	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
9	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
10	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv887417	chr7:5667645-5760860	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887418	chr7:5675305-5772551	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1028652	chr7:5706207-5769489	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5674800-5728200	Weak transcription	Small Intestine	intestine
2	chr7:5691200-5721000	Weak transcription	Pancreas	Pancrea
3	chr7:5692600-5717400	Weak transcription	Hela-S3	cervix
4	chr7:5699200-5723000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:5702000-5717600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:5702000-5730600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:5702400-5721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:5702600-5717400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:5702600-5717600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:5702600-5718000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:5702800-5727200	Weak transcription	Psoas Muscle	Psoas
12	chr7:5707600-5717400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:5707600-5717600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:5707600-5719000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:5707600-5721000	Weak transcription	Stomach Mucosa	stomach
16	chr7:5707800-5718000	Weak transcription	K562	blood
17	chr7:5708800-5717600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:5710600-5717600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:5710600-5718200	Weak transcription	Lung	lung
20	chr7:5710800-5717400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:5710800-5717600	Weak transcription	Colonic Mucosa	Colon
22	chr7:5710800-5721200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:5711400-5717600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:5711600-5717400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:5711600-5717400	Weak transcription	HSMMtube	muscle
26	chr7:5712400-5717400	Weak transcription	Primary B cells from cord blood	blood
27	chr7:5712600-5717400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:5712600-5717400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr7:5712600-5719200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:5712800-5717400	Weak transcription	Brain Anterior Caudate	brain
31	chr7:5713000-5730200	Weak transcription	Gastric	stomach
32	chr7:5713200-5717400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:5713200-5717400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:5713200-5717400	Weak transcription	Ovary	ovary
35	chr7:5713200-5717400	Weak transcription	Spleen	Spleen
36	chr7:5713200-5717600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:5713200-5718000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:5713200-5718200	Weak transcription	Dnd41	blood
39	chr7:5713200-5718800	Weak transcription	Thymus	Thymus
40	chr7:5713200-5719000	Weak transcription	Esophagus	oesophagus
41	chr7:5713200-5721400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:5713200-5724000	Weak transcription	Brain Germinal Matrix	brain
43	chr7:5713400-5717400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:5713400-5717400	Weak transcription	Fetal Lung	lung
45	chr7:5713400-5717600	Weak transcription	Fetal Brain Female	brain
46	chr7:5713400-5720600	Weak transcription	HepG2	liver
47	chr7:5713600-5717800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:5714000-5719200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:5715400-5723200	Enhancers	Adipose Nuclei	Adipose
50	chr7:5716000-5717400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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