Variant report

Variant	rs10270609
Chromosome Location	chr7:6311518-6311519
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6310725..6312409-chr7:6412991..6414709,2	K562	blood:
2	chr7:6214344..6218044-chr7:6310010..6312416,3	MCF-7	breast:
3	chr7:6206063..6207710-chr7:6310368..6312250,2	MCF-7	breast:
4	chr7:6143403..6145262-chr7:6310829..6313708,2	MCF-7	breast:
5	chr7:6217036..6219726-chr7:6310745..6313246,2	K562	blood:

Variant related genes	Relation type
ENSG00000238534	Chromatin interaction
ENSG00000106346	Chromatin interaction
ENSG00000008256	Chromatin interaction
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10245186	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10263878	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11976961	0.85[EUR][1000 genomes]
rs13237896	0.92[EUR][1000 genomes]
rs34073302	0.95[EUR][1000 genomes]
rs34312608	0.84[EUR][1000 genomes]
rs34904930	0.95[EUR][1000 genomes]
rs34939060	0.87[EUR][1000 genomes]
rs35257722	0.85[EUR][1000 genomes]
rs35372475	0.95[EUR][1000 genomes]
rs35402521	0.85[EUR][1000 genomes]
rs35719886	0.81[AFR][1000 genomes]
rs35868999	0.85[EUR][1000 genomes]
rs35882223	0.85[EUR][1000 genomes]
rs35934233	0.95[EUR][1000 genomes]
rs6463535	0.84[EUR][1000 genomes]
rs6463540	0.87[EUR][1000 genomes]
rs6955065	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6961095	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6962767	0.90[EUR][1000 genomes]
rs6969814	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71531366	0.85[EUR][1000 genomes]
rs71531367	0.85[EUR][1000 genomes]
rs71531368	0.85[EUR][1000 genomes]
rs71531370	0.85[EUR][1000 genomes]
rs71531372	0.95[EUR][1000 genomes]
rs71531373	0.92[EUR][1000 genomes]
rs71549618	0.95[EUR][1000 genomes]
rs7777433	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7780702	0.97[EUR][1000 genomes]
rs7783827	0.97[EUR][1000 genomes]
rs7791225	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
3	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
5	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
7	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
8	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1032987	chr7:6246313-6373054	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv538714	chr7:6246313-6373054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv538715	chr7:6308902-6359025	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv1020251	chr7:6309528-6379941	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv3401315	chr7:6311227-6313325	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10270609	PSCD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6309800-6312600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:6310200-6311600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:6310200-6311600	Flanking Active TSS	K562	blood
4	chr7:6310200-6312600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr7:6310400-6311600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:6310400-6311600	Flanking Active TSS	Fetal Brain Female	brain
7	chr7:6310400-6311600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr7:6310400-6311600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr7:6310400-6311600	Flanking Active TSS	NH-A	brain
10	chr7:6310400-6311800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr7:6310400-6311800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr7:6310400-6311800	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr7:6310400-6311800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:6310400-6311800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr7:6310400-6311800	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr7:6310400-6311800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr7:6310400-6311800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr7:6310400-6312000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:6310400-6312400	Active TSS	Brain Anterior Caudate	brain
20	chr7:6310400-6312400	Active TSS	Right Atrium	heart
21	chr7:6310400-6312600	Active TSS	Brain Cingulate Gyrus	brain
22	chr7:6310400-6312600	Active TSS	Brain Substantia Nigra	brain
23	chr7:6310400-6312600	Active TSS	Ovary	ovary
24	chr7:6310400-6312800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr7:6310400-6312800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:6310400-6312800	Active TSS	Aorta	Aorta
27	chr7:6310400-6312800	Active TSS	HSMMtube	muscle
28	chr7:6310600-6311600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr7:6310600-6311600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr7:6310600-6311600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr7:6310600-6311600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr7:6310600-6311600	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr7:6310600-6311600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr7:6310600-6311600	Flanking Active TSS	GM12878-XiMat	blood
35	chr7:6310600-6311600	Flanking Active TSS	Hela-S3	cervix
36	chr7:6310600-6311800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
37	chr7:6310600-6311800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr7:6310600-6311800	Flanking Active TSS	Liver	Liver
39	chr7:6310600-6312400	Active TSS	Brain Angular Gyrus	brain
40	chr7:6310600-6312400	Active TSS	HSMM	muscle
41	chr7:6310600-6312400	Active TSS	NHDF-Ad	bronchial
42	chr7:6310600-6312400	Active TSS	NHLF	lung
43	chr7:6310600-6312600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr7:6310600-6312600	Active TSS	Colon Smooth Muscle	Colon
45	chr7:6310600-6312600	Active TSS	Fetal Heart	heart
46	chr7:6310800-6311600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr7:6310800-6311600	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr7:6310800-6311600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:6310800-6311600	Flanking Bivalent TSS/Enh	Thymus	Thymus
50	chr7:6310800-6311800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links