Variant report

Variant	rs852420
Chromosome Location	chr7:5701591-5701592
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:5600355..5603301-chr7:5701063..5703061,2	K562	blood:
2	chr7:5694848..5697610-chr7:5699899..5703275,3	K562	blood:
3	chr7:5701115..5703280-chr7:5705262..5706862,2	K562	blood:
4	chr7:5562588..5565706-chr7:5701527..5703521,3	K562	blood:
5	chr7:5633053..5635244-chr7:5701549..5703673,2	K562	blood:
6	chr7:5697529..5700496-chr7:5700687..5702223,2	K562	blood:
7	chr7:5633681..5635608-chr7:5699910..5702357,2	MCF-7	breast:
8	chr7:5700345..5702615-chr7:5705262..5706869,2	K562	blood:
9	chr7:5697758..5700180-chr7:5700493..5702713,2	MCF-7	breast:
10	chr7:5563689..5568427-chr7:5701312..5705928,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228974	Chromatin interaction
ENSG00000263900	Chromatin interaction
ENSG00000075618	Chromatin interaction
ENSG00000075624	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10232762	0.83[EUR][1000 genomes]
rs10241310	1.00[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10259773	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1990836	0.82[AMR][1000 genomes]
rs2009260	0.80[AMR][1000 genomes]
rs2287593	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2287595	0.89[JPT][hapmap]
rs28417882	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801016	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3801019	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3823683	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4720640	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs4724713	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4724718	0.82[CEU][hapmap]
rs61203027	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6463506	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6463507	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6956960	0.83[EUR][1000 genomes]
rs6959871	0.82[CEU][hapmap]
rs6960381	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs6971289	0.89[JPT][hapmap]
rs710941	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777831	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7796461	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7800691	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7803308	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7804319	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs852257	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852258	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852265	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852266	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs852267	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs852375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs852397	1.00[CEU][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852402	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]
rs852409	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs852410	1.00[CEU][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs852415	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs852421	0.92[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852438	0.84[YRI][hapmap]
rs852441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852442	0.87[YRI][hapmap]
rs852448	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852450	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852457	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852461	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852472	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs852489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs852516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860425	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888582	0.82[AMR][1000 genomes]
rs888583	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9648578	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9691118	0.89[JPT][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	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
7	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
8	nsv1025434	chr7:5537571-5705283	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

No data

Chromatin state (count:123 , 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	chr7:5677200-5707200	Weak transcription	Stomach Mucosa	stomach
3	chr7:5677400-5706200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:5679200-5706000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:5679400-5701600	Weak transcription	Fetal Heart	heart
6	chr7:5683600-5710400	Weak transcription	Colonic Mucosa	Colon
7	chr7:5689800-5704000	Weak transcription	Fetal Brain Female	brain
8	chr7:5690200-5704000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:5690200-5706000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:5690400-5702400	Weak transcription	Psoas Muscle	Psoas
11	chr7:5690600-5704200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:5690600-5704200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:5690800-5704000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:5691000-5701600	Weak transcription	Right Ventricle	heart
15	chr7:5691000-5712000	Weak transcription	Fetal Kidney	kidney
16	chr7:5691200-5721000	Weak transcription	Pancreas	Pancrea
17	chr7:5691800-5701600	Weak transcription	Fetal Lung	lung
18	chr7:5692000-5701600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:5692200-5701600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:5692200-5701600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr7:5692200-5701600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:5692200-5704000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:5692400-5701600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:5692400-5701600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:5692600-5717400	Weak transcription	Hela-S3	cervix
26	chr7:5692800-5701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:5692800-5701600	Weak transcription	K562	blood
28	chr7:5692800-5702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:5692800-5702200	Weak transcription	Lung	lung
30	chr7:5695400-5701600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr7:5695400-5703800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:5695400-5703800	Strong transcription	Fetal Stomach	stomach
33	chr7:5695400-5704200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:5695400-5704600	Strong transcription	Fetal Intestine Small	intestine
35	chr7:5696000-5703000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:5697800-5704200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr7:5699200-5701600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:5699200-5701600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:5699200-5701600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:5699200-5702000	Weak transcription	Gastric	stomach
41	chr7:5699200-5723000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr7:5700200-5702800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:5700200-5702800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr7:5700200-5703000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:5700200-5704200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:5700400-5702600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:5700400-5702600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:5700400-5702600	Strong transcription	NH-A	brain
49	chr7:5700400-5702800	Strong transcription	Colon Smooth Muscle	Colon
50	chr7:5700600-5701600	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links