Variant report

Variant	rs342169
Chromosome Location	chr12:63086591-63086592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:63085784..63087372-chr12:63092972..63095214,2	MCF-7	breast:
2	chr12:63086305..63088144-chr12:63100380..63102991,2	MCF-7	breast:
3	chr12:63080648..63083389-chr12:63085536..63088456,3	MCF-7	breast:
4	chr12:63083624..63086955-chr12:63088722..63092795,3	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs163687	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1845375	0.90[JPT][hapmap]
rs2270483	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs342165	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs342167	0.90[EUR][1000 genomes]
rs342168	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs4763026	0.84[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4763027	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs61919541	0.91[EUR][1000 genomes]
rs72648149	0.89[EUR][1000 genomes]
rs7952978	0.84[CEU][hapmap]

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	nsv524555	chr12:63080231-63086591	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs342169	MARS	cis	parietal	SCAN
rs342169	DDIT3	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63067400-63116800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:63068800-63102800	Weak transcription	Right Ventricle	heart
3	chr12:63069400-63096600	Weak transcription	Fetal Kidney	kidney
4	chr12:63071400-63087000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:63071600-63087000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:63071600-63096400	Weak transcription	Left Ventricle	heart
7	chr12:63072000-63089200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:63074200-63092000	Strong transcription	HepG2	liver
9	chr12:63074600-63096400	Weak transcription	Pancreas	Pancrea
10	chr12:63077800-63086600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:63077800-63095400	Weak transcription	Placenta	Placenta
12	chr12:63078000-63118600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:63078200-63087200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:63078200-63087200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:63078200-63091600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:63078800-63086600	Weak transcription	Fetal Brain Male	brain
17	chr12:63078800-63087400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:63078800-63088200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:63079000-63087800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:63079000-63088000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:63079000-63096400	Weak transcription	Ovary	ovary
22	chr12:63079200-63087200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:63079200-63087200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:63079200-63095000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:63080000-63096400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:63080000-63096400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:63080800-63089400	Weak transcription	Thymus	Thymus
28	chr12:63081200-63086600	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:63081200-63093800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:63081400-63087000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:63081400-63087000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:63081600-63086600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:63082000-63087200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:63082000-63087400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:63082400-63091200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:63083200-63087000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:63083200-63087200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:63083600-63091400	Weak transcription	Adipose Nuclei	Adipose
39	chr12:63083800-63087400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:63083800-63094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:63083800-63103000	Weak transcription	Gastric	stomach
42	chr12:63084000-63086600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:63084000-63092000	Weak transcription	Brain Anterior Caudate	brain
44	chr12:63084200-63086600	Weak transcription	Fetal Stomach	stomach
45	chr12:63084400-63095000	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:63084800-63087200	Strong transcription	Fetal Intestine Large	intestine
47	chr12:63084800-63087400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:63085000-63087000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:63085200-63087000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:63085200-63095000	Weak transcription	Brain Substantia Nigra	brain

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