Variant report

Variant	rs12467474
Chromosome Location	chr2:33779062-33779063
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	chr2:33777937..33780353-chr2:33783539..33786426,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10186362	0.84[EUR][1000 genomes]
rs11884210	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12468045	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12470399	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12476217	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12476533	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12478596	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12478742	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13404493	0.87[EUR][1000 genomes]
rs17013237	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17013312	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4491711	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4491712	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55834207	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57542130	0.86[EUR][1000 genomes]
rs7574183	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516338	chr2:33758456-33780231	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12467474	RASGRP3	cis	Thyroid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33738600-33782800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:33740800-33790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr2:33747800-33780200	Weak transcription	Brain Anterior Caudate	brain
4	chr2:33748000-33790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:33748200-33780200	Weak transcription	Brain Angular Gyrus	brain
6	chr2:33755000-33779800	Weak transcription	Small Intestine	intestine
7	chr2:33755400-33779800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:33757000-33780000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:33757200-33809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:33760800-33782200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:33760800-33783600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:33761000-33789000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:33761200-33783800	Weak transcription	Psoas Muscle	Psoas
14	chr2:33762000-33780200	Weak transcription	Ovary	ovary
15	chr2:33762200-33779400	Weak transcription	Spleen	Spleen
16	chr2:33762200-33779600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:33762200-33809800	Weak transcription	Aorta	Aorta
18	chr2:33763200-33780200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:33765600-33784400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:33766800-33809800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:33767600-33779200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:33772600-33791000	Strong transcription	GM12878-XiMat	blood
23	chr2:33772600-33793400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:33773000-33779800	Weak transcription	Right Ventricle	heart
25	chr2:33774000-33790200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:33775200-33779800	Weak transcription	Fetal Heart	heart
27	chr2:33775600-33779200	Weak transcription	Left Ventricle	heart
28	chr2:33775600-33783400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:33775800-33779800	Weak transcription	Primary B cells from cord blood	blood
30	chr2:33776000-33809800	Weak transcription	Pancreas	Pancrea
31	chr2:33776200-33780000	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:33776200-33782800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:33776800-33779800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:33776800-33790600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:33777400-33779800	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:33777600-33780000	Enhancers	HUVEC	blood vessel
37	chr2:33777800-33783000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:33778000-33779800	Weak transcription	Placenta	Placenta
39	chr2:33778000-33780000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:33778000-33780000	Weak transcription	NHDF-Ad	bronchial
41	chr2:33778000-33781000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:33778000-33783600	Weak transcription	Fetal Intestine Small	intestine
43	chr2:33778000-33785200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:33778200-33779800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:33778200-33779800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr2:33778200-33784800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:33778400-33779200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:33778400-33779200	Weak transcription	Right Atrium	heart
49	chr2:33778400-33779400	Weak transcription	Lung	lung
50	chr2:33778400-33779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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