Variant report

Variant	rs34904930
Chromosome Location	chr7:6303711-6303712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6295146..6297854-chr7:6301609..6304566,2	MCF-7	breast:
2	chr7:6300982..6303712-chr7:6310025..6312320,4	MCF-7	breast:
3	chr7:6302141..6304166-chr7:6305919..6307712,2	K562	blood:

Variant related genes	Relation type
ENSG00000008256	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10245186	0.95[EUR][1000 genomes]
rs10263878	0.95[EUR][1000 genomes]
rs10270609	0.95[EUR][1000 genomes]
rs11976961	0.90[EUR][1000 genomes]
rs13237896	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34073302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34312608	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34939060	0.88[EUR][1000 genomes]
rs35257722	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35372475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35402521	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35868999	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35882223	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35934233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6463535	0.85[EUR][1000 genomes]
rs6463540	0.82[EUR][1000 genomes]
rs6955065	0.95[EUR][1000 genomes]
rs6961095	0.95[EUR][1000 genomes]
rs6962767	0.85[EUR][1000 genomes]
rs6969814	0.85[EUR][1000 genomes]
rs71531366	0.90[EUR][1000 genomes]
rs71531367	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71531368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71531370	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71531372	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71531373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71549618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7777433	0.92[EUR][1000 genomes]
rs7780702	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7783827	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7791225	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34904930	PSCD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6288200-6310400	Weak transcription	Brain Angular Gyrus	brain
2	chr7:6288400-6306600	Weak transcription	Esophagus	oesophagus
3	chr7:6293000-6306400	Weak transcription	NHEK	skin
4	chr7:6293400-6306600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:6296800-6308400	Weak transcription	HMEC	breast
6	chr7:6297600-6305400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:6298200-6306600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:6298400-6308600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:6299000-6310400	Weak transcription	Primary B cells from cord blood	blood
10	chr7:6299200-6310600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:6300000-6306800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:6300200-6308600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:6300200-6310200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:6300400-6306200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:6300400-6306200	Weak transcription	Gastric	stomach
16	chr7:6300400-6307600	Weak transcription	Pancreas	Pancrea
17	chr7:6300400-6308400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:6300400-6308600	Weak transcription	Aorta	Aorta
19	chr7:6300400-6310400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:6300600-6304200	Weak transcription	Right Ventricle	heart
21	chr7:6300600-6304600	Weak transcription	GM12878-XiMat	blood
22	chr7:6300600-6306600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr7:6300600-6306800	Weak transcription	A549	lung
24	chr7:6300600-6308600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:6300600-6310200	Weak transcription	Fetal Kidney	kidney
26	chr7:6300600-6310400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:6300800-6306200	Weak transcription	Placenta	Placenta
28	chr7:6300800-6306600	Weak transcription	Fetal Intestine Small	intestine
29	chr7:6300800-6308600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:6301000-6304000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:6301000-6308200	Weak transcription	Fetal Lung	lung
32	chr7:6301000-6309000	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:6301200-6304600	Weak transcription	Ovary	ovary
34	chr7:6301200-6306200	Weak transcription	Right Atrium	heart
35	chr7:6301200-6308800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:6301200-6310400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:6301200-6310400	Weak transcription	Colonic Mucosa	Colon
38	chr7:6302000-6310200	Weak transcription	NH-A	brain
39	chr7:6302200-6304200	Weak transcription	K562	blood
40	chr7:6302200-6306200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:6302200-6308400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:6302400-6304000	Enhancers	Fetal Muscle Trunk	muscle
43	chr7:6302400-6306400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:6302400-6310400	Weak transcription	Fetal Stomach	stomach
45	chr7:6302600-6303800	Weak transcription	Small Intestine	intestine
46	chr7:6302600-6304600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:6302600-6305800	Weak transcription	Left Ventricle	heart
48	chr7:6302600-6305800	Weak transcription	Psoas Muscle	Psoas
49	chr7:6302600-6308600	Weak transcription	NHLF	lung
50	chr7:6302600-6308800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links