Variant report

Variant	rs4660347
Chromosome Location	chr1:46913300-46913301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46912642..46915291-chr1:46916388..46919723,5	K562	blood:
2	chr1:46908179..46910338-chr1:46912412..46913923,2	K562	blood:
3	chr1:46910308..46913456-chr1:46992468..46994457,29	K562	blood:
4	chr1:46911278..46913612-chr1:46993367..46994439,12	MCF-7	breast:
5	chr1:46907167..46909679-chr1:46911926..46913949,3	K562	blood:
6	chr1:46911310..46914050-chr1:46990566..46993135,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KNCN-1	chr1:46913124-46913704	NONHSAT003015
2	lnc-KNCN-1	chr1:46913124-46913561	XLOC_000818

No data

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10890396	0.91[EUR][1000 genomes]
rs10890397	0.81[EUR][1000 genomes]
rs11211276	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211278	0.94[EUR][1000 genomes]
rs11211279	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12126376	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12407178	0.92[EUR][1000 genomes]
rs12409747	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2031248	0.82[EUR][1000 genomes]
rs2031249	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2281774	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2281775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404584	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3737742	0.84[LWK][hapmap];0.90[YRI][hapmap]
rs3795315	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4660929	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660933	0.82[EUR][1000 genomes]
rs4660935	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4660936	0.98[EUR][1000 genomes]
rs72637962	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538292	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7549865	1.00[YRI][hapmap]
rs868650	0.98[EUR][1000 genomes]
rs942258	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking 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	32 gene(s)	inside rSNPs	diseases
5	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv534951	chr1:46910546-46948727	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4660347	NSUN4	cis	cerebellum	SCAN
rs4660347	CCDC24	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46908800-46913400	Weak transcription	Spleen	Spleen
2	chr1:46909000-46913400	Weak transcription	Gastric	stomach
3	chr1:46909000-46913600	Weak transcription	Pancreas	Pancrea
4	chr1:46909000-46913800	Weak transcription	Right Atrium	heart
5	chr1:46911800-46913800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr1:46912000-46913400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr1:46912000-46913400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:46912400-46914600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:46912400-46915200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr1:46912600-46913400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
11	chr1:46912600-46914000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
12	chr1:46912600-46914400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr1:46912600-46914600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
14	chr1:46912600-46914600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:46912800-46913400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
16	chr1:46912800-46913400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:46912800-46913600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:46912800-46913600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:46912800-46913600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
20	chr1:46912800-46913800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr1:46912800-46913800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
22	chr1:46912800-46913800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
23	chr1:46912800-46913800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:46912800-46913800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:46912800-46913800	Bivalent Enhancer	Liver	Liver
26	chr1:46912800-46914000	Bivalent Enhancer	Colon Smooth Muscle	Colon
27	chr1:46912800-46914000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr1:46912800-46914000	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr1:46912800-46914600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr1:46912800-46914600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:46913000-46913600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:46913000-46913800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:46913000-46914000	Bivalent Enhancer	Brain Hippocampus Middle	brain
34	chr1:46913000-46914000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr1:46913000-46914000	Bivalent Enhancer	Placenta	Placenta
36	chr1:46913200-46913400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
37	chr1:46913200-46913400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
38	chr1:46913200-46913600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
39	chr1:46913200-46913600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:46913200-46913600	Bivalent Enhancer	Fetal Brain Female	brain
41	chr1:46913200-46914400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:46913200-46914800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr1:46913200-46915000	Weak transcription	K562	blood

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