Variant report

Variant	rs4840159
Chromosome Location	chr6:101330188-101330189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr6:101328620-101330270	Hela-S3	cervix:	n/a	n/a
2	MAX	chr6:101329874-101330267	K562	blood:	n/a	n/a
3	SETDB1	chr6:101328100-101330547	U2OS	brain:	n/a	n/a
4	POLR2A	chr6:101328660-101330218	K562	blood:	n/a	n/a
5	E2F6	chr6:101328552-101330245	H1-hESC	embryonic stem cell:	n/a	chr6:101329287-101329296 chr6:101329369-101329379 chr6:101329109-101329124 chr6:101328865-101328874 chr6:101329209-101329219 chr6:101329312-101329323 chr6:101329306-101329315
6	POLR2A	chr6:101328347-101330202	MCF10A-Er-Src	breast:	n/a	n/a
7	NFYB	chr6:101329907-101330340	GM12878	blood:	n/a	n/a
8	KAP1	chr6:101328380-101330607	HEK293	kidney:	n/a	n/a
9	HCFC1	chr6:101327729-101330325	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr6:101327954-101330323	SK-N-SH	brain:	n/a	n/a
11	MAFF	chr6:101330017-101330260	K562	blood:	n/a	n/a
12	POLR2A	chr6:101328338-101330279	HepG2	liver:	n/a	n/a
13	MAFK	chr6:101330168-101330288	K562	blood:	n/a	n/a
14	RCOR1	chr6:101328789-101330626	K562	blood:	n/a	n/a
15	USF2	chr6:101329966-101330429	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:101327744-101330641	GM12891	blood:	n/a	n/a
17	MAZ	chr6:101328643-101330415	IMR90	lung:	n/a	chr6:101329314-101329324 chr6:101329135-101329142
18	MAZ	chr6:101329874-101330324	K562	blood:	n/a	n/a
19	TBL1XR1	chr6:101330163-101330500	K562	blood:	n/a	n/a
20	MAX	chr6:101328515-101330264	A549	lung:	n/a	chr6:101329314-101329324 chr6:101329135-101329142

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101328677..101332841-chr6:101334376..101338552,5	K562	blood:
2	chr6:101326886..101330925-chr6:101337161..101339877,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRIK2-2	chr6:101329347-101330847	ENSG00000260000.1
2	lnc-GRIK2-2	chr6:101329347-101330863	ENSG00000260000.2

Variant related genes	Relation type
ASCC3	TF binding region
ENSG00000270987	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1069049	0.83[JPT][hapmap]
rs11155720	0.82[ASN][1000 genomes]
rs11755579	0.80[EUR][1000 genomes]
rs11758174	0.80[EUR][1000 genomes]
rs12174782	0.83[JPT][hapmap]
rs12530388	0.92[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1813223	0.80[EUR][1000 genomes]
rs34555037	0.80[EUR][1000 genomes]
rs4454144	0.96[ASN][1000 genomes]
rs4840157	0.80[EUR][1000 genomes]
rs592436	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs618919	0.81[ASN][1000 genomes]
rs657915	0.83[JPT][hapmap]
rs664245	0.80[CHB][hapmap]
rs6908709	1.00[YRI][hapmap]
rs6919745	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6934256	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs705591	0.95[ASN][1000 genomes]
rs705599	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs705605	0.83[JPT][hapmap]
rs705607	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs705608	0.83[JPT][hapmap]
rs705610	0.81[ASN][1000 genomes]
rs723742	0.84[CEU][hapmap]
rs7739574	0.83[JPT][hapmap]
rs7750098	0.83[JPT][hapmap]
rs7771570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs846777	0.94[ASN][1000 genomes]
rs846794	0.83[JPT][hapmap]
rs846797	0.81[JPT][hapmap]
rs846798	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs9322294	0.86[ASN][1000 genomes]
rs9377240	0.80[EUR][1000 genomes]
rs9404055	0.85[YRI][hapmap]
rs9404059	0.81[EUR][1000 genomes]
rs9498419	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9498420	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs979122	0.81[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised 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
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4840159	LIN28B	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101326600-101330200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:101327000-101330200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:101327400-101330200	Active TSS	A549	lung
4	chr6:101327400-101330200	Active TSS	HSMM	muscle
5	chr6:101327400-101330200	Active TSS	NHDF-Ad	bronchial
6	chr6:101327400-101330200	Active TSS	NHLF	lung
7	chr6:101327400-101330600	Active TSS	GM12878-XiMat	blood
8	chr6:101327400-101330800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:101327800-101330400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:101328000-101330200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:101328000-101330200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:101328000-101330200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:101328000-101330400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:101328200-101330200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:101328200-101330200	Active TSS	Brain Substantia Nigra	brain
16	chr6:101328200-101330200	Active TSS	Stomach Smooth Muscle	stomach
17	chr6:101328400-101330200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:101328600-101330200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:101329400-101330200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:101329400-101330200	Active TSS	Aorta	Aorta
21	chr6:101329400-101330200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr6:101329400-101330200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr6:101329400-101330600	Active TSS	Right Atrium	heart
24	chr6:101329600-101330200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:101329600-101330200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:101329600-101330200	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr6:101329600-101330200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr6:101329600-101330200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr6:101329600-101330200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:101329600-101330200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:101329600-101330200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr6:101329600-101330200	Flanking Active TSS	Liver	Liver
33	chr6:101329600-101330200	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr6:101329600-101330200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr6:101329600-101330200	Enhancers	Spleen	Spleen
36	chr6:101329600-101330200	Flanking Active TSS	HUVEC	blood vessel
37	chr6:101329600-101330400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:101329600-101330400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr6:101329600-101330400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:101329600-101330400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:101329600-101330800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:101329600-101330800	Enhancers	Small Intestine	intestine
43	chr6:101329800-101330200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr6:101329800-101330200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
45	chr6:101329800-101330200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr6:101329800-101330200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr6:101329800-101330200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr6:101329800-101330200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr6:101329800-101330200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:101329800-101330200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links