Variant report

Variant	rs218966
Chromosome Location	chr7:11022230-11022231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:10993482..10995624-chr7:11021410..11023892,2	K562	blood:
2	chr7:11013321..11019837-chr7:11020708..11025466,8	MCF-7	breast:
3	chr7:10908452..10910556-chr7:11019934..11022818,2	K562	blood:
4	chr7:10978217..10981674-chr7:11020968..11026596,6	K562	blood:

Variant related genes	Relation type
ENSG00000271185	Chromatin interaction
ENSG00000189043	Chromatin interaction
ENSG00000106443	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10239092	0.81[EUR][1000 genomes]
rs10239754	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1079478	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1154921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1640701	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1640702	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1640703	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1640705	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1640708	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1640712	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1640713	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681286	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1681299	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1681311	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs190075	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1989161	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218962	0.80[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs218965	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs218967	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs218969	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs218971	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs218974	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs218976	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs218982	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs218983	0.92[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs220096	0.81[ASN][1000 genomes]
rs6943604	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6943989	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6951303	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7807585	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067780	chr7:10649696-11329787	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
2	nsv491695	chr7:10649696-11329787	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats 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
4	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
5	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
6	nsv532092	chr7:10731350-11414759	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv887600	chr7:10807685-11090546	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv949387	chr7:10815994-11281536	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS 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	26 gene(s)	inside rSNPs	diseases
10	esv2752140	chr7:10817060-11029748	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1029882	chr7:10872162-11371145	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	27 gene(s)	inside rSNPs	diseases
12	nsv817291	chr7:10875417-11562683	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv1031498	chr7:10882696-11110412	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv887601	chr7:10912949-11049523	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs218966	GLCCI1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11014200-11038600	Weak transcription	Small Intestine	intestine
2	chr7:11014400-11031800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:11014400-11033200	Weak transcription	Left Ventricle	heart
4	chr7:11014600-11032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:11014600-11035000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:11014600-11035000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:11014600-11035000	Weak transcription	Placenta	Placenta
8	chr7:11014600-11035200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:11014600-11038600	Weak transcription	Psoas Muscle	Psoas
10	chr7:11014600-11045400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr7:11014600-11092000	Weak transcription	Colonic Mucosa	Colon
12	chr7:11014800-11026400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:11014800-11032200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:11014800-11032600	Weak transcription	Osteobl	bone
15	chr7:11014800-11033000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:11014800-11033000	Weak transcription	Brain Hippocampus Middle	brain
17	chr7:11014800-11033400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr7:11014800-11034600	Weak transcription	HMEC	breast
19	chr7:11014800-11035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:11014800-11039200	Weak transcription	Brain Substantia Nigra	brain
21	chr7:11014800-11054200	Weak transcription	NHLF	lung
22	chr7:11014800-11075200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:11014800-11117400	Weak transcription	HSMMtube	muscle
24	chr7:11015000-11022400	Weak transcription	Fetal Intestine Large	intestine
25	chr7:11015000-11029200	Weak transcription	Fetal Intestine Small	intestine
26	chr7:11015000-11034000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr7:11015000-11037400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:11015000-11037400	Weak transcription	NHEK	skin
29	chr7:11015000-11064000	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:11015200-11108200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr7:11015600-11022400	Weak transcription	Primary B cells from cord blood	blood
32	chr7:11015600-11032200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:11015800-11022600	Weak transcription	NHDF-Ad	bronchial
34	chr7:11016000-11022400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:11016000-11033400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:11016400-11022400	Weak transcription	HSMM	muscle
37	chr7:11016800-11031600	Weak transcription	A549	lung
38	chr7:11016800-11057200	Weak transcription	Fetal Brain Male	brain
39	chr7:11017200-11076000	Weak transcription	HUVEC	blood vessel
40	chr7:11017800-11037200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr7:11018600-11026400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr7:11018600-11035200	Weak transcription	Aorta	Aorta
43	chr7:11018600-11063800	Weak transcription	Brain Angular Gyrus	brain
44	chr7:11019800-11022400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:11020000-11022400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:11020800-11026600	Strong transcription	Dnd41	blood
47	chr7:11020800-11037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr7:11021000-11023600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:11021200-11023600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:11021200-11026200	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links