Variant report

Variant	rs240588
Chromosome Location	chr22:34024097-34024098
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:34017891..34021270-chr22:34021737..34025602,3	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1029297	0.85[CEU][hapmap]
rs11089627	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs171275	0.84[ASN][1000 genomes]
rs2051567	0.81[CEU][hapmap]
rs2239746	0.84[CEU][hapmap]
rs2267238	0.81[CEU][hapmap]
rs2267239	0.84[CEU][hapmap]
rs2267241	0.81[CEU][hapmap]
rs2283922	0.84[CEU][hapmap]
rs2283924	0.84[CEU][hapmap]
rs240589	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240590	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs240591	0.81[CEU][hapmap]
rs240592	0.81[CEU][hapmap]
rs240593	0.84[CEU][hapmap]
rs240595	0.81[CEU][hapmap]
rs240597	0.81[CEU][hapmap]
rs2413196	1.00[YRI][hapmap]
rs4239873	0.81[CEU][hapmap]
rs5749634	0.84[CEU][hapmap]
rs6518833	0.84[CEU][hapmap]
rs695366	0.84[CEU][hapmap]
rs695509	0.84[CEU][hapmap]
rs718682	0.81[CEU][hapmap]
rs738962	0.84[CEU][hapmap]
rs738964	0.84[CEU][hapmap]
rs762859	0.80[CEU][hapmap]
rs86487	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv914983	chr22:33800119-34035034	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1060283	chr22:33809137-34043739	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv544684	chr22:33809137-34043739	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1065417	chr22:33823850-34053325	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv933309	chr22:33825232-34053000	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
13	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv914987	chr22:33920421-34047427	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv588934	chr22:33965639-34035034	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv914988	chr22:33975998-34083987	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv934161	chr22:33979015-34118621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv588935	chr22:34008430-34073758	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv914989	chr22:34011334-34083987	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs240588	LIMK2	cis	cerebellum	SCAN
rs240588	C22orf24	cis	cerebellum	SCAN
rs240588	DEPDC5	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33965200-34045800	Weak transcription	Pancreas	Pancrea
2	chr22:33994000-34029600	Weak transcription	Aorta	Aorta
3	chr22:33994200-34050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr22:33995800-34049800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr22:34003000-34062400	Weak transcription	Gastric	stomach
6	chr22:34007200-34050400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:34008000-34031000	Weak transcription	Fetal Intestine Small	intestine
8	chr22:34008000-34039400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr22:34010000-34025200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr22:34010200-34029800	Weak transcription	GM12878-XiMat	blood
11	chr22:34014200-34029000	Weak transcription	Right Ventricle	heart
12	chr22:34016200-34033000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr22:34016200-34046000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr22:34017000-34026000	Weak transcription	Fetal Brain Female	brain
15	chr22:34017000-34050400	Weak transcription	Colonic Mucosa	Colon
16	chr22:34017800-34036000	Weak transcription	Brain Hippocampus Middle	brain
17	chr22:34017800-34047800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:34018600-34032200	Weak transcription	Spleen	Spleen
19	chr22:34018600-34045600	Weak transcription	Colon Smooth Muscle	Colon
20	chr22:34018800-34033200	Weak transcription	Psoas Muscle	Psoas
21	chr22:34019400-34036800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr22:34019400-34050600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr22:34019600-34029400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:34019600-34035400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:34020800-34045000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr22:34021200-34029200	Weak transcription	Fetal Stomach	stomach
27	chr22:34021200-34031400	Weak transcription	Fetal Intestine Large	intestine
28	chr22:34021200-34037000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr22:34021200-34045600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr22:34021400-34024400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr22:34021400-34034800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr22:34021400-34035000	Weak transcription	Liver	Liver
33	chr22:34021400-34038800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr22:34021400-34044600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr22:34021400-34045600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr22:34021400-34053000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr22:34021600-34033000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr22:34021600-34033400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr22:34021600-34034400	Weak transcription	Left Ventricle	heart
40	chr22:34021600-34037000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr22:34021600-34044800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr22:34021600-34045400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr22:34021800-34033200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr22:34022200-34032400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr22:34022200-34041000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr22:34022400-34033000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr22:34022400-34035000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr22:34022600-34044800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr22:34023000-34035200	Weak transcription	Ovary	ovary
50	chr22:34023400-34027600	Weak transcription	Fetal Heart	heart

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