Variant report

Variant	rs2244022
Chromosome Location	chr7:66202430-66202431
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10234018	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs10249404	0.89[CEU][hapmap];0.95[YRI][hapmap]
rs10252765	0.89[CEU][hapmap];0.86[GIH][hapmap];0.94[LWK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs10263935	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs10950044	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs11028	0.82[YRI][hapmap]
rs13227951	0.86[GIH][hapmap]
rs13308803	0.83[CEU][hapmap]
rs1553610	0.94[YRI][hapmap]
rs2013222	0.89[CEU][hapmap]
rs2191268	0.89[CEU][hapmap];0.86[GIH][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs2286683	0.89[CEU][hapmap]
rs2707845	0.85[CEU][hapmap];0.95[YRI][hapmap]
rs2707852	0.87[YRI][hapmap]
rs2707853	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs2707854	0.81[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs2707856	0.81[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs3764903	0.81[ASW][hapmap];0.89[CEU][hapmap];0.86[GIH][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs3800812	0.89[CEU][hapmap];0.95[YRI][hapmap]
rs3800820	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs4273746	0.85[CEU][hapmap]
rs6460305	0.81[ASW][hapmap];0.89[CEU][hapmap];0.86[GIH][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs6460308	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs6943696	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs6947808	0.85[YRI][hapmap]
rs6952407	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs6958520	0.81[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs7793569	0.89[CEU][hapmap];0.95[YRI][hapmap]
rs801205	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs801217	0.89[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh 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
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
6	nsv971490	chr7:66192193-66212423	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2244022	C19orf50	trans	parietal	SCAN
rs2244022	ZNF117	cis	cerebellum	SCAN
rs2244022	KCTD7	cis	parietal	SCAN
rs2244022	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2244022	RABGEF1	cis	cerebellum	SCAN
rs2244022	ZNF273	cis	cerebellum	SCAN
rs2244022	GUSB	cis	parietal	SCAN
rs2244022	ZNF138	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66165400-66204600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:66176400-66204600	Weak transcription	Colonic Mucosa	Colon
3	chr7:66179600-66204600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:66182800-66205000	Weak transcription	Gastric	stomach
5	chr7:66190400-66204600	Weak transcription	Stomach Mucosa	stomach
6	chr7:66190800-66204400	Weak transcription	Fetal Heart	heart
7	chr7:66190800-66204600	Weak transcription	NHEK	skin
8	chr7:66191200-66204600	Weak transcription	NHLF	lung
9	chr7:66191200-66205000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:66191400-66204600	Weak transcription	Primary T cells from cord blood	blood
11	chr7:66191600-66204600	Weak transcription	NHDF-Ad	bronchial
12	chr7:66191800-66204800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:66193800-66204800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:66194000-66204800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:66194000-66205000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:66194000-66205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:66194600-66204600	Weak transcription	Fetal Kidney	kidney
18	chr7:66194600-66205000	Weak transcription	Spleen	Spleen
19	chr7:66195600-66204800	Weak transcription	Lung	lung
20	chr7:66197000-66204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:66197400-66202800	Weak transcription	Right Atrium	heart
22	chr7:66197400-66204600	Weak transcription	Right Ventricle	heart
23	chr7:66199200-66203000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:66199600-66204800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:66200600-66202600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:66200600-66204600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:66200800-66203600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:66200800-66205000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr7:66201000-66203000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:66201200-66204600	Weak transcription	Fetal Intestine Large	intestine
31	chr7:66201200-66204800	Enhancers	Primary B cells from peripheral blood	blood
32	chr7:66201400-66202600	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:66201400-66203800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:66201400-66204200	Weak transcription	Fetal Thymus	thymus
35	chr7:66201400-66204600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:66201400-66204600	Weak transcription	Fetal Lung	lung
37	chr7:66201600-66202600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:66201600-66202600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:66201600-66202600	Weak transcription	Ovary	ovary
40	chr7:66201600-66202600	Enhancers	GM12878-XiMat	blood
41	chr7:66201600-66202800	Weak transcription	Brain Substantia Nigra	brain
42	chr7:66201600-66203200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr7:66201600-66203400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:66201600-66203400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:66201600-66203400	Weak transcription	Liver	Liver
46	chr7:66201600-66203600	Weak transcription	Brain Anterior Caudate	brain
47	chr7:66201600-66203800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr7:66201600-66203800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:66201600-66203800	Weak transcription	Dnd41	blood
50	chr7:66201600-66204200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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