Variant report

Variant	rs140126
Chromosome Location	chr22:30147038-30147039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30130941..30133818-chr22:30144985..30147499,2	MCF-7	breast:
2	chr22:30145045..30147687-chr22:30166151..30168873,2	MCF-7	breast:
3	chr22:30142692..30145269-chr22:30145289..30147345,2	K562	blood:
4	chr22:30144477..30147071-chr22:30161090..30163905,2	K562	blood:

Variant related genes	Relation type
ENSG00000184076	Chromatin interaction
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs105311	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131260	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131261	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131262	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs131263	0.92[ASN][1000 genomes]
rs131264	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131265	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131266	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131267	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131270	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131271	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131272	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131273	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131274	0.90[ASN][1000 genomes]
rs131275	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs131277	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131279	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs131281	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs131282	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs131284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131285	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.89[ASN][1000 genomes]
rs131286	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs131287	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131298	0.88[EUR][1000 genomes]
rs131301	0.83[CHB][hapmap]
rs140094	0.88[JPT][hapmap]
rs140095	0.90[ASN][1000 genomes]
rs140096	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs140097	0.91[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs140099	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs140100	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs140101	0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.94[ASN][1000 genomes]
rs140102	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140103	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs140104	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140107	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140110	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs140111	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs140113	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140114	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140117	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs140118	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs140119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140120	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs140121	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140122	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs140123	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140124	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140127	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140129	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140130	0.81[EUR][1000 genomes]
rs140131	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs140133	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs140134	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140139	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140140	0.85[EUR][1000 genomes]
rs140145	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs140149	0.83[CHB][hapmap]
rs1961926	0.81[CEU][hapmap]
rs2074706	0.83[CHB][hapmap]
rs2074707	0.83[CHB][hapmap]
rs249396	0.86[EUR][1000 genomes]
rs249397	0.85[EUR][1000 genomes]
rs249398	0.83[CHB][hapmap]
rs249401	0.83[EUR][1000 genomes]
rs36572	0.86[EUR][1000 genomes]
rs36576	0.83[CHB][hapmap];0.86[MEX][hapmap]
rs5752961	0.83[CHB][hapmap]
rs5752962	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs5752964	0.83[CHB][hapmap]
rs5763512	0.83[CHB][hapmap]
rs5997530	0.83[CHB][hapmap]
rs6006267	0.85[GIH][hapmap]
rs713656	0.83[CHB][hapmap]
rs713657	0.83[CHB][hapmap]
rs740041	0.83[CHB][hapmap]
rs7954	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs81800	0.83[CHB][hapmap];0.80[CHD][hapmap];0.86[MEX][hapmap]
rs9306465	0.83[CHB][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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs140126	CABP7	cis	cerebellum	SCAN
rs140126	NIPSNAP1	cis	cerebellum	SCAN
rs140126	KIAA1671	cis	cerebellum	SCAN
rs140126	CRYBB3	cis	parietal	SCAN
rs140126	NIPSNAP1	cis	parietal	SCAN
rs140126	UCRC	cis	multi-tissue	Pritchard
rs140126	MTMR3	Cis_1M	lymphoblastoid	RTeQTL
rs140126	TTC28AS	cis	cerebellum	SCAN
rs140126	INPP5J	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30130200-30150200	Weak transcription	A549	lung
2	chr22:30130400-30150600	Strong transcription	Fetal Intestine Small	intestine
3	chr22:30130600-30149800	Weak transcription	Psoas Muscle	Psoas
4	chr22:30131400-30148600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr22:30131600-30162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:30131800-30147200	Strong transcription	Brain Inferior Temporal Lobe	brain
7	chr22:30134400-30158400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:30136000-30154800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:30141200-30150800	Strong transcription	Fetal Brain Female	brain
10	chr22:30141600-30154200	Weak transcription	Osteobl	bone
11	chr22:30141800-30147200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr22:30141800-30155400	Strong transcription	Fetal Stomach	stomach
13	chr22:30142000-30150000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr22:30142600-30147400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr22:30143600-30147200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr22:30143600-30154200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr22:30144000-30147800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr22:30144400-30148400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr22:30144400-30150000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr22:30144400-30150000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr22:30144400-30161800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr22:30144400-30162000	Weak transcription	Placenta	Placenta
23	chr22:30144400-30162200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr22:30144600-30148000	Weak transcription	Spleen	Spleen
25	chr22:30144600-30148600	Weak transcription	Fetal Intestine Large	intestine
26	chr22:30144600-30149800	Weak transcription	Thymus	Thymus
27	chr22:30144600-30150000	Weak transcription	Brain Angular Gyrus	brain
28	chr22:30144600-30160000	Weak transcription	Dnd41	blood
29	chr22:30144600-30161800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr22:30144600-30161800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr22:30144600-30161800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr22:30144600-30162000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:30144800-30148000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr22:30144800-30149400	Weak transcription	Fetal Lung	lung
35	chr22:30144800-30149800	Weak transcription	Brain Hippocampus Middle	brain
36	chr22:30144800-30150000	Weak transcription	HSMM	muscle
37	chr22:30144800-30155000	Weak transcription	Ovary	ovary
38	chr22:30144800-30161800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr22:30144800-30161800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:30144800-30161800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr22:30145000-30150200	Weak transcription	HSMMtube	muscle
42	chr22:30145200-30154000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr22:30145400-30154200	Weak transcription	NHDF-Ad	bronchial
44	chr22:30145600-30149800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr22:30146000-30147200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr22:30146000-30147400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr22:30146000-30150800	Strong transcription	Primary T cells from cord blood	blood
48	chr22:30146000-30161800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr22:30146200-30147400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:30146200-30148200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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