Variant report

Variant	rs852397
Chromosome Location	chr7:5719557-5719558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5630491..5634130-chr7:5717559..5720896,4	K562	blood:
2	chr7:5696126..5698767-chr7:5718167..5720079,2	MCF-7	breast:
3	chr7:5631406..5634130-chr7:5717559..5720896,4	K562	blood:
4	chr7:5567652..5570729-chr7:5716334..5720767,4	MCF-7	breast:
5	chr7:5707603..5710385-chr7:5717513..5719879,2	K562	blood:

Variant related genes	Relation type
ENSG00000075618	Chromatin interaction
ENSG00000263900	Chromatin interaction
ENSG00000075624	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

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];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259773	0.93[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	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11531468	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12531598	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1990836	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2009260	0.90[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];0.91[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	0.91[AFR][1000 genomes]
rs3735289	1.00[ASN][1000 genomes]
rs3801016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3801019	0.89[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	0.89[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	0.88[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	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6463506	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463507	0.82[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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[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	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6971289	0.88[MEX][hapmap]
rs710941	0.85[AMR][1000 genomes]
rs7777831	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795879	0.86[JPT][hapmap]
rs7796461	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800691	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803308	0.91[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	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852258	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852265	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[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];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852267	0.95[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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852376	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852396	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs852402	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	0.91[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];0.93[YRI][hapmap];0.95[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];0.93[YRI][hapmap];0.94[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];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852421	0.83[EUR][1000 genomes]
rs852438	0.83[YRI][hapmap]
rs852441	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][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	0.81[AFR][1000 genomes];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];0.89[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	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888583	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648578	0.90[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs852397	C7orf27	cis	cerebellum	SCAN

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	chr7:5699200-5723000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:5702000-5730600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:5702400-5721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:5702800-5727200	Weak transcription	Psoas Muscle	Psoas
7	chr7:5707600-5721000	Weak transcription	Stomach Mucosa	stomach
8	chr7:5710800-5721200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:5713000-5730200	Weak transcription	Gastric	stomach
10	chr7:5713200-5721400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:5713200-5724000	Weak transcription	Brain Germinal Matrix	brain
12	chr7:5713400-5720600	Weak transcription	HepG2	liver
13	chr7:5715400-5723200	Enhancers	Adipose Nuclei	Adipose
14	chr7:5716000-5720000	Enhancers	Rectal Smooth Muscle	rectum
15	chr7:5716000-5720600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:5716200-5719800	Genic enhancers	Fetal Stomach	stomach
17	chr7:5716200-5721800	Enhancers	Right Atrium	heart
18	chr7:5716400-5719600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:5716400-5722000	Enhancers	Fetal Heart	heart
20	chr7:5716600-5719800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr7:5716600-5722400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:5716800-5719600	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr7:5716800-5719800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:5716800-5719800	Enhancers	Fetal Thymus	thymus
25	chr7:5716800-5720000	Enhancers	Liver	Liver
26	chr7:5716800-5724000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr7:5717000-5720200	Genic enhancers	Fetal Intestine Small	intestine
28	chr7:5717000-5723200	Enhancers	Placenta	Placenta
29	chr7:5717200-5723400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr7:5717200-5726600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr7:5717400-5719600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:5717400-5719600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:5717400-5719600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr7:5717400-5719800	Enhancers	Primary hematopoietic stem cells	blood
35	chr7:5717400-5719800	Enhancers	Fetal Lung	lung
36	chr7:5717400-5720600	Enhancers	Primary B cells from cord blood	blood
37	chr7:5717400-5720800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr7:5717400-5723000	Weak transcription	Aorta	Aorta
39	chr7:5717400-5723800	Enhancers	Primary B cells from peripheral blood	blood
40	chr7:5717600-5720800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:5717600-5722600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:5717600-5722600	Weak transcription	Fetal Kidney	kidney
43	chr7:5717600-5723800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:5717600-5726600	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr7:5717600-5727600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr7:5717800-5719600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:5717800-5722400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:5717800-5722600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr7:5717800-5723000	Weak transcription	NHLF	lung
50	chr7:5717800-5723800	Weak transcription	Hela-S3	cervix

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