Variant report

Variant	rs2550749
Chromosome Location	chr16:81425153-81425154
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81418335..81421743-chr16:81423347..81426141,3	MCF-7	breast:
2	chr16:81417073..81419356-chr16:81422898..81425873,2	K562	blood:
3	chr16:81422912..81425576-chr16:81496658..81498919,2	K562	blood:

Variant related genes	Relation type
ENSG00000272923	Chromatin interaction
ENSG00000273048	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11647874	0.85[GIH][hapmap]
rs12448327	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs182559	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs192835	0.87[EUR][1000 genomes]
rs1981884	0.85[GIH][hapmap]
rs2446084	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2550738	0.83[CEU][hapmap]
rs2550746	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2608555	0.84[GIH][hapmap]
rs2608562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615701	0.83[CEU][hapmap]
rs2927314	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs310022	0.81[EUR][1000 genomes]
rs310024	0.86[EUR][1000 genomes]
rs310025	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs310032	0.91[CEU][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs3127538	0.99[EUR][1000 genomes]
rs4889307	0.85[GIH][hapmap]
rs6564871	0.92[GIH][hapmap]
rs7191409	0.85[GIH][hapmap]
rs7630	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9928509	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1061359	chr16:81349826-81471867	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv542992	chr16:81349826-81471867	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2550749	GAN	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81384200-81434600	Weak transcription	NHLF	lung
2	chr16:81384200-81437400	Weak transcription	Fetal Brain Male	brain
3	chr16:81387000-81428600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:81392000-81428400	Weak transcription	Fetal Heart	heart
5	chr16:81397400-81426400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr16:81399200-81431000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr16:81400000-81427200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:81400000-81434600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr16:81411200-81428400	Weak transcription	GM12878-XiMat	blood
10	chr16:81411400-81428000	Weak transcription	Spleen	Spleen
11	chr16:81411400-81428200	Weak transcription	Stomach Mucosa	stomach
12	chr16:81411400-81429200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr16:81411400-81429600	Weak transcription	HSMM	muscle
14	chr16:81411600-81428600	Weak transcription	Fetal Kidney	kidney
15	chr16:81411600-81437400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr16:81411800-81428200	Weak transcription	Fetal Brain Female	brain
17	chr16:81411800-81428200	Weak transcription	Osteobl	bone
18	chr16:81411800-81428600	Weak transcription	HSMMtube	muscle
19	chr16:81411800-81431000	Weak transcription	K562	blood
20	chr16:81411800-81432400	Weak transcription	A549	lung
21	chr16:81412000-81426200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr16:81412200-81425400	Weak transcription	NH-A	brain
23	chr16:81412200-81425600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr16:81412200-81434400	Weak transcription	Hela-S3	cervix
25	chr16:81412400-81425200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr16:81412400-81425600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:81412600-81426600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr16:81412600-81427000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:81412600-81427200	Weak transcription	NHDF-Ad	bronchial
30	chr16:81413000-81428400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr16:81413400-81425800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr16:81413400-81434200	Weak transcription	HMEC	breast
33	chr16:81414000-81426600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr16:81415200-81427600	Weak transcription	Primary B cells from cord blood	blood
35	chr16:81415600-81437000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr16:81417800-81426600	Weak transcription	Brain Angular Gyrus	brain
37	chr16:81418000-81426000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr16:81418200-81427200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr16:81418200-81427600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr16:81418200-81437200	Weak transcription	Colon Smooth Muscle	Colon
41	chr16:81418600-81426600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr16:81418600-81427800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr16:81418600-81430600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr16:81418600-81431000	Weak transcription	Brain Germinal Matrix	brain
45	chr16:81418600-81437400	Weak transcription	Fetal Lung	lung
46	chr16:81419000-81426200	Strong transcription	Fetal Intestine Small	intestine
47	chr16:81419000-81426600	Strong transcription	Fetal Stomach	stomach
48	chr16:81419000-81428400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr16:81419000-81429400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr16:81419200-81427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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