Variant report

Variant	rs404523
Chromosome Location	chr7:101724053-101724054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101723290..101725556-chr7:101728286..101729955,2	K562	blood:
2	chr7:101722804..101725007-chr7:101742245..101744915,2	K562	blood:
3	chr7:101714618..101716441-chr7:101723476..101725531,2	K562	blood:
4	chr7:101714618..101716538-chr7:101724031..101725533,2	K562	blood:
5	chr7:101717039..101718587-chr7:101722028..101724096,2	K562	blood:
6	chr7:101706528..101709517-chr7:101721356..101724154,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10268506	1.00[CHB][hapmap]
rs365397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375417	0.87[CEU][hapmap]
rs376183	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs377587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377612	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406012	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs409420	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs411844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412332	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412524	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413348	1.00[ASN][1000 genomes]
rs420709	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs421154	1.00[ASN][1000 genomes]
rs421430	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425577	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294126	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430154	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432002	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432600	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438908	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441160	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443159	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443293	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729771	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56960461	0.92[AFR][1000 genomes]
rs57164493	0.92[AFR][1000 genomes]
rs58868901	0.88[AFR][1000 genomes]
rs73185898	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408006	0.92[AFR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs404523	BRI3	cis	cerebellum	SCAN
rs404523	C7orf59	cis	parietal	SCAN
rs404523	CUX1	cis	cerebellum	SCAN
rs404523	ZKSCAN5	cis	parietal	SCAN
rs404523	TRIP6	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101707200-101738000	Weak transcription	Colon Smooth Muscle	Colon
2	chr7:101708200-101765000	Weak transcription	Small Intestine	intestine
3	chr7:101708400-101726000	Weak transcription	NHEK	skin
4	chr7:101715200-101725800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:101715200-101728600	Weak transcription	Colonic Mucosa	Colon
6	chr7:101715200-101749800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:101715400-101749600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:101715600-101724200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:101715600-101725000	Weak transcription	Ovary	ovary
10	chr7:101715600-101725200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:101715600-101725200	Weak transcription	HSMM	muscle
12	chr7:101715600-101725800	Weak transcription	Adipose Nuclei	Adipose
13	chr7:101715600-101726400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:101715600-101728600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr7:101715600-101745200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:101715600-101745200	Weak transcription	HSMMtube	muscle
17	chr7:101715800-101726000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:101715800-101732600	Weak transcription	Fetal Kidney	kidney
19	chr7:101715800-101732800	Weak transcription	Aorta	Aorta
20	chr7:101715800-101741000	Weak transcription	Gastric	stomach
21	chr7:101715800-101741200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:101716000-101725200	Weak transcription	NHLF	lung
23	chr7:101716000-101736600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:101716000-101743000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:101716000-101746600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:101716400-101724200	Weak transcription	Osteobl	bone
27	chr7:101716400-101758600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:101717800-101741200	Weak transcription	Pancreas	Pancrea
29	chr7:101718000-101724200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:101718000-101732800	Weak transcription	Esophagus	oesophagus
31	chr7:101718600-101725000	Weak transcription	Lung	lung
32	chr7:101718600-101736600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:101718800-101724200	Weak transcription	Primary B cells from cord blood	blood
34	chr7:101719000-101724200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr7:101719200-101724200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:101719200-101726000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:101720200-101725000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:101720600-101725200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr7:101720800-101725000	Weak transcription	GM12878-XiMat	blood
40	chr7:101720800-101732600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:101721000-101724200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr7:101721200-101726600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr7:101721800-101724400	Enhancers	Fetal Heart	heart
44	chr7:101722000-101724400	Enhancers	NH-A	brain
45	chr7:101722000-101726000	Strong transcription	Thymus	Thymus
46	chr7:101722400-101724400	Enhancers	Placenta	Placenta
47	chr7:101722400-101726600	Strong transcription	Primary T cells from cord blood	blood
48	chr7:101722600-101726000	Strong transcription	Dnd41	blood
49	chr7:101722800-101724800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:101722800-101725200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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