Variant report

Variant	rs6730949
Chromosome Location	chr2:46978056-46978057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46977061..46979853-chr2:46982842..46984764,2	K562	blood:
2	chr2:46965000..46967486-chr2:46976098..46978644,2	K562	blood:
3	chr2:46969632..46972292-chr2:46976605..46978764,2	K562	blood:
4	chr2:46930029..46933528-chr2:46976256..46980348,3	K562	blood:
5	chr2:46970114..46972113-chr2:46977401..46980359,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1009230	0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs1009231	0.91[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10167561	0.89[ASN][1000 genomes]
rs10168342	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125087	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12466948	0.84[ASN][1000 genomes]
rs12475080	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1456009	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1471056	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1471057	0.82[ASN][1000 genomes]
rs1809216	0.84[ASN][1000 genomes]
rs1813505	0.88[ASN][1000 genomes]
rs1867819	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs2045291	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2061182	0.85[ASN][1000 genomes]
rs3738890	0.81[ASN][1000 genomes]
rs3768720	0.80[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3814039	0.83[ASN][1000 genomes]
rs4361172	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4522653	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953414	0.81[ASN][1000 genomes]
rs4953415	0.90[ASN][1000 genomes]
rs4953418	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544913	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6544917	0.83[ASN][1000 genomes]
rs6544918	0.93[ASN][1000 genomes]
rs6544919	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6544921	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6705847	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6718658	0.83[YRI][hapmap]
rs6718677	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721122	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6726345	0.98[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6727737	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6727934	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6728559	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6740539	0.85[YRI][hapmap]
rs6741706	0.88[ASN][1000 genomes]
rs6746471	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6748938	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7568007	0.87[ASN][1000 genomes]
rs7570376	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7580649	0.89[ASN][1000 genomes]
rs897528	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs958726	0.87[ASN][1000 genomes]
rs970711	0.82[MEX][hapmap]
rs991559	0.83[ASN][1000 genomes]
rs991742	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv3459561	chr2:46967674-46979121	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv3459562	chr2:46967674-46979121	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	esv14887	chr2:46967820-46978960	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	esv2760650	chr2:46970686-46978878	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6730949	SOCS5	cis	multi-tissue	Pritchard
rs6730949	RPL18A	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:46955200-46984800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr2:46955200-46985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:46956000-46980000	Weak transcription	Right Atrium	heart
5	chr2:46960000-46978800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:46960000-46988000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:46962000-46982000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:46964800-46985800	Weak transcription	Primary B cells from cord blood	blood
9	chr2:46965400-46979200	Weak transcription	Psoas Muscle	Psoas
10	chr2:46965600-46980800	Weak transcription	Fetal Heart	heart
11	chr2:46965800-46986800	Weak transcription	Hela-S3	cervix
12	chr2:46968000-46979200	Weak transcription	Left Ventricle	heart
13	chr2:46968000-46980000	Weak transcription	Spleen	Spleen
14	chr2:46969400-46988200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:46972600-46981000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:46972600-46986600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:46973200-46981400	Enhancers	NHDF-Ad	bronchial
18	chr2:46973400-46985600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:46973600-46980000	Enhancers	Osteobl	bone
20	chr2:46974200-46983000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:46974400-46980000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:46974600-46990000	Weak transcription	Colonic Mucosa	Colon
23	chr2:46974800-46980200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:46974800-46985600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:46974800-46986600	Weak transcription	Gastric	stomach
26	chr2:46975000-46979000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:46975000-46979200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:46975000-46979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:46975000-46980400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:46975000-46985400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:46975000-46986800	Weak transcription	GM12878-XiMat	blood
32	chr2:46975200-46979000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:46975600-46985400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:46975600-46985400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:46975600-46985400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:46975600-46985400	Weak transcription	Lung	lung
37	chr2:46975600-46986000	Weak transcription	Esophagus	oesophagus
38	chr2:46975600-46986400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:46975800-46979000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:46975800-46979200	Weak transcription	Right Ventricle	heart
41	chr2:46975800-46986800	Weak transcription	Pancreas	Pancrea
42	chr2:46976200-46979200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:46976200-46984800	Weak transcription	Fetal Intestine Small	intestine
44	chr2:46976200-46990400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:46976400-46979000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:46976400-46980400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:46976400-46980400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:46976400-46980800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:46976400-46980800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:46976400-46985400	Weak transcription	Monocytes-CD14+_RO01746	blood

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