Variant report

Variant	rs7973541
Chromosome Location	chr12:51464845-51464846
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51442447..51444522-chr12:51464420..51466543,2	K562	blood:
2	chr12:51461592..51467381-chr12:51474203..51479524,7	K562	blood:
3	chr12:51460740..51468069-chr12:51474538..51479190,12	MCF-7	breast:
4	chr12:51464271..51466652-chr12:51600358..51602044,2	MCF-7	breast:
5	chr12:51459011..51461192-chr12:51463959..51465473,2	K562	blood:

Variant related genes	Relation type
ENSG00000050426	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000184271	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1026994	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10747603	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10783411	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10783412	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768959	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6580783	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7972608	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7974923	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975628	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9739943	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7973541	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:51444200-51465000	Strong transcription	Fetal Muscle Leg	muscle
4	chr12:51444200-51465400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:51444200-51465600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:51444200-51470400	Strong transcription	Fetal Stomach	stomach
7	chr12:51445000-51467800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:51445400-51467800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:51445400-51467800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr12:51445400-51469200	Strong transcription	Fetal Thymus	thymus
11	chr12:51445400-51470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:51445600-51465200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr12:51445600-51467400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr12:51445600-51467800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:51445600-51467800	Strong transcription	Adipose Nuclei	Adipose
16	chr12:51445600-51468000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr12:51445600-51468400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:51445600-51469200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:51445600-51469800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:51445600-51470400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:51445600-51470600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:51445800-51468000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:51445800-51468400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:51446000-51468400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:51446800-51468600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:51447000-51466800	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:51447400-51468400	Strong transcription	Fetal Lung	lung
28	chr12:51449200-51467800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:51449800-51470000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:51450200-51468600	Strong transcription	Osteobl	bone
31	chr12:51452800-51468000	Strong transcription	Fetal Brain Female	brain
32	chr12:51453400-51470600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:51454000-51475400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:51454200-51470400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:51454200-51475600	Weak transcription	Stomach Mucosa	stomach
36	chr12:51454600-51467800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:51455000-51467800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr12:51455000-51467800	Strong transcription	NH-A	brain
39	chr12:51455000-51468600	Strong transcription	Thymus	Thymus
40	chr12:51455200-51465200	Strong transcription	HSMMtube	muscle
41	chr12:51455200-51467800	Strong transcription	Brain Angular Gyrus	brain
42	chr12:51455200-51467800	Strong transcription	Ovary	ovary
43	chr12:51455400-51470400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:51455400-51470800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:51455600-51467800	Strong transcription	Brain Hippocampus Middle	brain
46	chr12:51455600-51470400	Strong transcription	Brain Germinal Matrix	brain
47	chr12:51456400-51470400	Strong transcription	Fetal Intestine Small	intestine
48	chr12:51459000-51471400	Weak transcription	Fetal Heart	heart
49	chr12:51459000-51475600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr12:51459800-51469400	Weak transcription	Small Intestine	intestine

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