Variant report

Variant	rs394384
Chromosome Location	chr12:51403649-51403650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51396990..51399929-chr12:51402029..51404417,2	K562	blood:
2	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:
3	chr12:51397539..51404278-chr12:51405080..51409503,9	MCF-7	breast:
4	chr12:51403202..51405028-chr12:51412638..51414252,2	MCF-7	breast:
5	chr12:51403352..51405981-chr12:51411330..51414858,3	K562	blood:

Variant related genes	Relation type
ENSG00000272028	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1026994	1.00[ASN][1000 genomes]
rs10747603	1.00[ASN][1000 genomes]
rs10783411	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10783412	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10876126	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095997	0.90[AMR][1000 genomes]
rs11169679	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423207	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814178	0.81[AFR][1000 genomes]
rs150909	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161046	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125367	0.82[CEU][hapmap]
rs17125370	0.82[CEU][hapmap]
rs17229232	0.82[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029147	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046498	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224564	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224569	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224585	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs224586	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs224592	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224593	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554858	0.81[AMR][1000 genomes]
rs2554859	0.85[AMR][1000 genomes]
rs2630358	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630362	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630366	0.95[AMR][1000 genomes]
rs2630367	0.95[AMR][1000 genomes]
rs319930	0.95[AMR][1000 genomes]
rs319938	0.90[YRI][hapmap];0.95[AMR][1000 genomes]
rs319943	0.82[CEU][hapmap]
rs364627	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416062	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768959	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4768967	0.82[YRI][hapmap]
rs55874852	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs58309379	1.00[ASN][1000 genomes]
rs613977	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618510	0.85[EUR][1000 genomes]
rs6580779	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.83[EUR][1000 genomes]
rs6580783	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs686528	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.82[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs706804	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7299484	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968372	0.80[EUR][1000 genomes]
rs7969536	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.85[EUR][1000 genomes]
rs7971712	0.82[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975117	0.90[AMR][1000 genomes]
rs7975628	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs7978782	1.00[YRI][hapmap]
rs829021	0.82[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs853236	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9739943	0.88[AFR][1000 genomes];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs394384	SLC11A2	cis	multi-tissue	Pritchard
rs394384	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51386000-51406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:51388600-51406600	Weak transcription	Small Intestine	intestine
4	chr12:51389400-51405400	Weak transcription	Esophagus	oesophagus
5	chr12:51390000-51405800	Weak transcription	Stomach Mucosa	stomach
6	chr12:51399000-51406200	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:51399200-51404400	Weak transcription	NH-A	brain
8	chr12:51399200-51418000	Weak transcription	Gastric	stomach
9	chr12:51399400-51408200	Weak transcription	NHDF-Ad	bronchial
10	chr12:51399600-51405800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:51399600-51405800	Weak transcription	Spleen	Spleen
12	chr12:51399800-51405200	Weak transcription	HUVEC	blood vessel
13	chr12:51399800-51406800	Weak transcription	A549	lung
14	chr12:51399800-51414600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:51399800-51415600	Weak transcription	Right Ventricle	heart
16	chr12:51400000-51407200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:51400000-51407400	Weak transcription	HMEC	breast
18	chr12:51401000-51410800	Weak transcription	HepG2	liver
19	chr12:51401200-51403800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:51401600-51410000	Weak transcription	Pancreas	Pancrea
22	chr12:51402000-51405400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:51402000-51405400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
26	chr12:51402200-51403800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr12:51402400-51405200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr12:51402400-51405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:51402400-51405600	Weak transcription	NHEK	skin
30	chr12:51402400-51405800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:51402400-51406200	Weak transcription	Fetal Lung	lung
32	chr12:51402400-51406400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:51402400-51407200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:51402400-51407200	Weak transcription	Lung	lung
35	chr12:51402400-51408600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:51402400-51415600	Weak transcription	GM12878-XiMat	blood
37	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
39	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:51402600-51403800	Enhancers	Brain Germinal Matrix	brain
41	chr12:51402600-51403800	Enhancers	Dnd41	blood
42	chr12:51402600-51404000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr12:51402600-51404600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:51402600-51405800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:51402600-51406400	Enhancers	Fetal Brain Male	brain
46	chr12:51402600-51406800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr12:51402800-51403800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr12:51402800-51404800	Enhancers	Fetal Brain Female	brain
49	chr12:51403000-51403800	Enhancers	Primary hematopoietic stem cells	blood
50	chr12:51403000-51403800	Enhancers	Liver	Liver

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