Variant report

Variant	rs201523
Chromosome Location	chr7:101771851-101771852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:101764947..101767456-chr7:101770353..101773289,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs169307	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1902	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201435	0.92[CEU][hapmap]
rs201441	0.92[CEU][hapmap]
rs201442	0.92[CEU][hapmap]
rs201443	0.92[CEU][hapmap]
rs201445	0.92[CEU][hapmap]
rs201447	0.92[CEU][hapmap]
rs201448	0.92[CEU][hapmap]
rs201449	0.92[CEU][hapmap]
rs201450	0.92[CEU][hapmap]
rs201454	0.92[CEU][hapmap]
rs201455	0.92[CEU][hapmap]
rs201456	0.92[CEU][hapmap]
rs201459	0.91[CEU][hapmap]
rs201468	0.92[CEU][hapmap]
rs201469	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs201470	0.87[ASN][1000 genomes]
rs201471	0.87[ASN][1000 genomes]
rs201472	0.84[ASN][1000 genomes]
rs201475	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs201477	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs201478	0.90[ASN][1000 genomes]
rs201480	0.90[ASN][1000 genomes]
rs201481	0.90[ASN][1000 genomes]
rs201482	0.90[ASN][1000 genomes]
rs201490	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs201491	0.96[CEU][hapmap]
rs201493	0.87[CEU][hapmap]
rs201498	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs201500	0.90[ASN][1000 genomes]
rs201502	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs201503	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs201504	0.90[ASN][1000 genomes]
rs201505	0.90[ASN][1000 genomes]
rs201509	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs201511	0.88[ASN][1000 genomes]
rs201514	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201516	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201517	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201521	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201522	0.92[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs201526	0.88[ASN][1000 genomes]
rs201527	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs201529	0.85[ASN][1000 genomes]
rs201530	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs417013	0.85[JPT][hapmap]
rs436287	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6950791	0.92[CEU][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs201523	CUX1	cis	cerebellum	SCAN
rs201523	MANF	trans	cerebellum	SCAN
rs201523	ATXN7L1	cis	parietal	SCAN
rs201523	ZCWPW1	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101755200-101787000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:101755400-101773200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:101760200-101796000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:101760400-101788600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:101760400-101789400	Weak transcription	Right Ventricle	heart
6	chr7:101760400-101795800	Weak transcription	Left Ventricle	heart
7	chr7:101761000-101795600	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:101763400-101772200	Weak transcription	Fetal Brain Female	brain
9	chr7:101763600-101773200	Weak transcription	Fetal Kidney	kidney
10	chr7:101763600-101790400	Weak transcription	Brain Anterior Caudate	brain
11	chr7:101765200-101788600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:101765200-101801200	Weak transcription	Pancreas	Pancrea
13	chr7:101765400-101777200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr7:101765400-101780000	Weak transcription	Small Intestine	intestine
15	chr7:101765600-101773000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr7:101765600-101783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:101765600-101801000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:101765800-101783800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr7:101766000-101773600	Strong transcription	Dnd41	blood
20	chr7:101766000-101773800	Strong transcription	Fetal Stomach	stomach
21	chr7:101766000-101777000	Weak transcription	Fetal Lung	lung
22	chr7:101766000-101784600	Weak transcription	HUVEC	blood vessel
23	chr7:101766000-101796000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:101766000-101796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:101766000-101796000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr7:101766200-101772400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr7:101766200-101772600	Strong transcription	Fetal Thymus	thymus
28	chr7:101766200-101772800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:101766200-101773200	Weak transcription	Psoas Muscle	Psoas
30	chr7:101766200-101777200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr7:101766200-101777200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:101766200-101777600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:101766200-101779400	Weak transcription	Colonic Mucosa	Colon
34	chr7:101766200-101781000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr7:101766200-101793800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:101766200-101796000	Weak transcription	Esophagus	oesophagus
37	chr7:101766200-101796600	Weak transcription	Brain Germinal Matrix	brain
38	chr7:101766400-101777000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:101766600-101774800	Strong transcription	Fetal Intestine Small	intestine
40	chr7:101766800-101773600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr7:101767200-101772000	Strong transcription	Primary T cells from cord blood	blood
42	chr7:101767200-101772600	Strong transcription	Thymus	Thymus
43	chr7:101767200-101773200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr7:101767400-101773600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:101768000-101775400	Weak transcription	HepG2	liver
46	chr7:101768000-101777600	Weak transcription	Primary B cells from cord blood	blood
47	chr7:101768000-101793800	Weak transcription	K562	blood
48	chr7:101768800-101772400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:101768800-101772400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:101768800-101773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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