Variant report

Variant	rs6488285
Chromosome Location	chr12:10518706-10518707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10518506..10519182-chr16:20688297..20688797,2	HCT-116	colon:

Extended variants
information (count: 59 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs1049172	0.86[CHD][hapmap]
rs10743887	0.82[ASN][1000 genomes]
rs10743888	0.87[EUR][1000 genomes]
rs10743889	0.86[EUR][1000 genomes]
rs10772267	0.82[JPT][hapmap]
rs1351113	0.86[CHD][hapmap]
rs1382264	0.93[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs1382265	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs1478309	0.93[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs1478310	0.88[EUR][1000 genomes]
rs1600127	0.90[EUR][1000 genomes]
rs2045876	0.88[EUR][1000 genomes]
rs2100923	0.86[EUR][1000 genomes]
rs2126888	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2126889	0.90[EUR][1000 genomes]
rs2246809	0.93[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2255336	0.93[CEU][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs2255353	0.90[EUR][1000 genomes]
rs2255364	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs2417734	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2617151	0.93[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs2617152	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2617156	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2617157	0.90[EUR][1000 genomes]
rs2617169	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2617172	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2733840	0.93[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733845	0.93[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2733847	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2733848	0.84[EUR][1000 genomes]
rs2733853	0.84[EUR][1000 genomes]
rs2734414	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs2734561	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2927561	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs4415856	1.00[JPT][hapmap]
rs4764430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139147	0.82[ASN][1000 genomes]
rs7301582	1.00[JPT][hapmap]
rs7307721	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7310643	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7397310	0.87[EUR][1000 genomes]
rs7956385	0.82[ASN][1000 genomes]
rs7957681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959328	0.82[ASN][1000 genomes]
rs7964772	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965744	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7980379	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3432683	chr12:10470734-10527581	Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
5	esv3351751	chr12:10472734-10522269	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription 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	9 gene(s)	inside rSNPs	diseases
10	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv898763	chr12:10514528-10603670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6488285	KLRK1	cis	lymphoblastoid	seeQTL
rs6488285	KLRC4	cis	cerebellum	SCAN
rs6488285	LRRC23	cis	cerebellum	SCAN
rs6488285	GNB3	cis	cerebellum	SCAN
rs6488285	KLRC4	cis	lesional skin	skin_eQTL
rs6488285	KLRK1	cis	parietal	SCAN
rs6488285	ZNF384	cis	cerebellum	SCAN
rs6488285	CHD4	cis	cerebellum	SCAN
rs6488285	KLRC2	cis	parietal	SCAN
rs6488285	KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs6488285	KLRC3	cis	parietal	SCAN
rs6488285	KLRC4	cis	parietal	SCAN
rs6488285	C12orf53	cis	cerebellum	SCAN
rs6488285	KLRC2	cis	cerebellum	SCAN
rs6488285	C1S	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10516200-10518800	Flanking Active TSS	HUVEC	blood vessel
2	chr12:10516400-10519200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:10516600-10518800	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr12:10516600-10518800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:10517800-10518800	Flanking Active TSS	Osteobl	bone
6	chr12:10517800-10519000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:10517800-10519600	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr12:10518000-10518800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr12:10518000-10519200	Flanking Active TSS	Hela-S3	cervix
10	chr12:10518000-10519400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:10518200-10518800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:10518200-10518800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:10518200-10518800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr12:10518200-10518800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:10518200-10518800	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr12:10518200-10518800	Flanking Active TSS	HMEC	breast
17	chr12:10518200-10518800	Flanking Active TSS	HSMM	muscle
18	chr12:10518200-10519000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:10518200-10519000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr12:10518200-10519200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr12:10518200-10519200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:10518200-10519200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:10518200-10519200	Enhancers	Spleen	Spleen
24	chr12:10518200-10519200	Flanking Active TSS	NHDF-Ad	bronchial
25	chr12:10518200-10519200	Flanking Active TSS	NHEK	skin
26	chr12:10518200-10519400	Enhancers	Esophagus	oesophagus
27	chr12:10518200-10519400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr12:10518200-10519400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr12:10518200-10519600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr12:10518200-10519600	Enhancers	Placenta	Placenta
31	chr12:10518200-10519800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr12:10518400-10518800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:10518400-10518800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr12:10518400-10518800	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr12:10518400-10518800	Flanking Active TSS	HepG2	liver
36	chr12:10518400-10519000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:10518400-10519000	Enhancers	GM12878-XiMat	blood
38	chr12:10518400-10519200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:10518400-10519200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:10518400-10519200	Enhancers	Aorta	Aorta
41	chr12:10518400-10519200	Enhancers	Gastric	stomach
42	chr12:10518400-10519200	Enhancers	Right Ventricle	heart
43	chr12:10518400-10519400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:10518400-10519400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:10518400-10519400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:10518400-10519400	Enhancers	Fetal Muscle Leg	muscle
47	chr12:10518400-10519400	Enhancers	Fetal Thymus	thymus
48	chr12:10518400-10519400	Enhancers	Pancreas	Pancrea
49	chr12:10518400-10519400	Enhancers	Psoas Muscle	Psoas
50	chr12:10518400-10519400	Flanking Active TSS	K562	blood

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