Variant report

Variant	rs778341
Chromosome Location	chr2:233728801-233728802
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233725993..233729161-chr2:233734807..233736601,3	K562	blood:
2	chr2:233727449..233731351-chr2:233736566..233741117,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182600	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1078323	1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs1083522	0.93[ASW][hapmap];0.91[CEU][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10933406	0.95[YRI][hapmap]
rs1104764	0.95[YRI][hapmap]
rs11535	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11688166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11689851	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12105766	0.80[ASW][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap]
rs12619195	0.95[YRI][hapmap]
rs13007579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13009957	0.90[ASN][1000 genomes]
rs13024330	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs1446309	1.00[CHB][hapmap]
rs17164	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs1973675	0.80[ASW][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs2289911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2344613	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675953	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2675954	0.93[ASW][hapmap];0.91[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2675955	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2675968	0.93[ASW][hapmap];0.95[CEU][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs283470	0.95[YRI][hapmap]
rs4973563	0.90[ASN][1000 genomes]
rs4973564	0.80[ASW][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs4973569	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704763	0.80[ASW][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap]
rs6717048	0.95[YRI][hapmap]
rs6733495	0.95[YRI][hapmap]
rs709937	0.95[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs737027	0.95[YRI][hapmap]
rs748002	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs7560115	0.87[ASN][1000 genomes]
rs778370	0.93[ASW][hapmap];0.95[CEU][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs778371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921055	1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs938569	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs938575	0.91[CEU][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs778341	IQCA1	cis	parietal	SCAN
rs778341	TIGD1	cis	parietal	SCAN
rs778341	CAB39	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:233722800-233738000	Weak transcription	Stomach Mucosa	stomach
4	chr2:233723000-233733200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:233723000-233740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:233723200-233733200	Weak transcription	Small Intestine	intestine
7	chr2:233723200-233736600	Weak transcription	Colonic Mucosa	Colon
8	chr2:233723200-233738600	Weak transcription	K562	blood
9	chr2:233723600-233729800	Weak transcription	HUVEC	blood vessel
10	chr2:233723600-233734200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:233723600-233735200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:233723600-233736400	Weak transcription	Right Ventricle	heart
13	chr2:233723600-233736600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:233724000-233729200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:233724000-233729600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:233724000-233734600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:233724000-233736000	Weak transcription	Fetal Brain Male	brain
18	chr2:233724200-233732200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:233724200-233733800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:233724200-233738600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:233724400-233734200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:233724600-233729600	Weak transcription	Aorta	Aorta
23	chr2:233724600-233734200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:233724600-233738600	Weak transcription	Esophagus	oesophagus
25	chr2:233724800-233732800	Weak transcription	Hela-S3	cervix
26	chr2:233724800-233734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:233725000-233735800	Weak transcription	Fetal Thymus	thymus
28	chr2:233726000-233729400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:233726000-233730400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:233726000-233733400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:233726000-233737400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:233726000-233740400	Weak transcription	HMEC	breast
33	chr2:233726200-233735000	Weak transcription	Brain Angular Gyrus	brain
34	chr2:233726200-233735600	Weak transcription	Osteobl	bone
35	chr2:233726200-233737400	Weak transcription	Fetal Brain Female	brain
36	chr2:233726400-233729600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:233726400-233729600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:233726400-233730600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:233726400-233731000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:233726400-233731400	Weak transcription	Ovary	ovary
41	chr2:233726400-233732200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:233726400-233732400	Weak transcription	Fetal Kidney	kidney
43	chr2:233726400-233733000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:233726400-233734400	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:233726400-233735000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:233726400-233735000	Weak transcription	Spleen	Spleen
47	chr2:233726400-233736000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:233726400-233736200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:233726400-233736200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:233726400-233738200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links