Variant report

Variant	rs613977
Chromosome Location	chr12:51410303-51410304
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51409891..51411468-chr12:51419026..51421501,2	K562	blood:
2	chr12:51406751..51409668-chr12:51409825..51412277,3	MCF-7	breast:
3	chr12:51410218..51413195-chr12:51416479..51420227,4	MCF-7	breast:
4	chr12:51157130..51159042-chr12:51410041..51412870,2	K562	blood:
5	chr12:51408556..51414296-chr12:51415375..51421759,13	MCF-7	breast:
6	chr12:51405834..51407705-chr12:51409196..51411163,3	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000272028	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1026994	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10747603	1.00[ASN][1000 genomes]
rs10783411	1.00[ASN][1000 genomes]
rs10783412	1.00[ASN][1000 genomes]
rs10876126	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169679	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423207	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs150909	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161046	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17229232	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029147	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046498	0.84[EUR][1000 genomes]
rs224564	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224569	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224585	0.92[EUR][1000 genomes]
rs224586	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.94[EUR][1000 genomes]
rs224592	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224593	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630358	0.84[EUR][1000 genomes]
rs2630362	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364627	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416062	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.98[EUR][1000 genomes]
rs4768959	1.00[ASN][1000 genomes]
rs58309379	1.00[ASN][1000 genomes]
rs618510	0.90[EUR][1000 genomes]
rs6580779	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.89[EUR][1000 genomes]
rs6580783	1.00[ASN][1000 genomes]
rs686528	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.88[EUR][1000 genomes]
rs706804	0.88[EUR][1000 genomes]
rs7299484	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968372	0.82[EUR][1000 genomes]
rs7969536	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.90[EUR][1000 genomes]
rs7971712	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[ASN][1000 genomes]
rs7975628	1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs829021	0.88[EUR][1000 genomes]
rs853236	0.84[EUR][1000 genomes]
rs9739943	0.90[EUR][1000 genomes];1.00[ASN][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
rs613977	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:51399200-51418000	Weak transcription	Gastric	stomach
3	chr12:51399800-51414600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:51399800-51415600	Weak transcription	Right Ventricle	heart
5	chr12:51401000-51410800	Weak transcription	HepG2	liver
6	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
9	chr12:51402400-51415600	Weak transcription	GM12878-XiMat	blood
10	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
12	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:51403400-51415600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:51403600-51412000	Weak transcription	Fetal Intestine Small	intestine
17	chr12:51403600-51414200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:51403600-51414400	Weak transcription	Hela-S3	cervix
19	chr12:51403600-51414600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:51403600-51417600	Weak transcription	HSMM	muscle
22	chr12:51403800-51411200	Weak transcription	Fetal Intestine Large	intestine
23	chr12:51403800-51412800	Weak transcription	Primary T cells from cord blood	blood
24	chr12:51403800-51412800	Weak transcription	Dnd41	blood
25	chr12:51403800-51417000	Weak transcription	Brain Germinal Matrix	brain
26	chr12:51404000-51411400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:51404200-51411200	Weak transcription	Fetal Thymus	thymus
28	chr12:51404200-51411200	Weak transcription	Ovary	ovary
29	chr12:51404200-51411200	Weak transcription	Thymus	Thymus
30	chr12:51404200-51414600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
32	chr12:51405800-51415000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:51406000-51414600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:51406000-51415200	Weak transcription	Right Atrium	heart
35	chr12:51406400-51417200	Weak transcription	Fetal Brain Male	brain
36	chr12:51406400-51417400	Weak transcription	Osteobl	bone
37	chr12:51406400-51417600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:51406600-51413800	Weak transcription	Brain Anterior Caudate	brain
39	chr12:51406800-51414200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:51406800-51415000	Weak transcription	Fetal Heart	heart
41	chr12:51407000-51412800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:51407000-51412800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:51407000-51414800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:51407000-51417400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:51407000-51417600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:51407200-51415800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:51407400-51411000	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:51407400-51411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:51407400-51412800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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