Variant report

Variant	rs2340802
Chromosome Location	chr6:149348504-149348505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149348124..149349985-chr6:149399476..149401160,2	MCF-7	breast:
2	chr5:141348409..141350133-chr6:149347981..149349666,2	MCF-7	breast:
3	chr6:149348466..149350718-chr6:149745093..149747617,2	MCF-7	breast:
4	chr6:149348139..149350308-chr6:149866371..149868197,2	MCF-7	breast:
5	chr6:149339358..149341194-chr6:149347879..149350031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131013	Chromatin interaction
ENSG00000113555	Chromatin interaction
ENSG00000013561	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10457074	0.91[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1317171	0.82[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs1934224	0.86[CEU][hapmap];0.83[TSI][hapmap]
rs2275423	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2340751	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2340752	0.95[CEU][hapmap];0.83[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2340798	0.81[CEU][hapmap]
rs2340801	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2879843	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4318907	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4377808	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4897074	0.91[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4897076	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570920	0.95[CEU][hapmap];0.83[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6904550	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6915298	0.82[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap]
rs6930989	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6931675	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs6931744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935330	0.82[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap]
rs6936176	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7747463	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7748978	0.83[CHB][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7761119	0.86[GIH][hapmap];0.91[MEX][hapmap]
rs7765778	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774457	0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7774887	0.95[CEU][hapmap];0.83[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7776117	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs9285516	0.86[GIH][hapmap];0.96[MEX][hapmap]
rs9377187	0.95[CEU][hapmap];0.83[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9377188	0.83[CHB][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9399678	0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2340802	C6orf97	cis	cerebellum	SCAN
rs2340802	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149321800-149349800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:149334000-149353400	Weak transcription	Spleen	Spleen
5	chr6:149334400-149352800	Weak transcription	HSMMtube	muscle
6	chr6:149336200-149349800	Weak transcription	Brain Anterior Caudate	brain
7	chr6:149336200-149351400	Weak transcription	Fetal Thymus	thymus
8	chr6:149336200-149353000	Weak transcription	Pancreas	Pancrea
9	chr6:149336200-149353200	Weak transcription	Esophagus	oesophagus
10	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:149336400-149354000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:149336800-149353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:149337200-149353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:149337600-149352800	Weak transcription	NHLF	lung
15	chr6:149337600-149353000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:149337600-149358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:149338200-149351800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:149338200-149352400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:149338800-149350000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:149339400-149353200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:149339400-149364600	Weak transcription	Lung	lung
22	chr6:149339800-149353200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:149341000-149353400	Weak transcription	Aorta	Aorta
24	chr6:149341000-149365400	Weak transcription	Right Ventricle	heart
25	chr6:149341200-149352200	Weak transcription	Primary T cells from cord blood	blood
26	chr6:149341400-149353200	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:149342400-149353400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:149343000-149352800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:149343200-149352400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:149343200-149358000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:149343400-149349800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:149344000-149352000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:149344000-149352800	Weak transcription	Fetal Lung	lung
34	chr6:149344000-149353000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:149344000-149357200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:149344000-149357400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:149344600-149353400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:149344600-149353600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:149344600-149353800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:149344600-149357800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:149344800-149354800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr6:149344800-149358000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:149345000-149352800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:149345000-149353000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:149345000-149355200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:149345200-149349800	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:149345400-149350400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:149345400-149353000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:149345400-149353000	Weak transcription	Fetal Stomach	stomach
50	chr6:149345400-149353600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links