Variant report

Variant	rs2630362
Chromosome Location	chr12:51378408-51378409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51377924..51379984-chr12:51420251..51421770,2	MCF-7	breast:
2	chr12:51377579..51380145-chr12:51442153..51443726,2	K562	blood:
3	chr12:51375354..51377058-chr12:51377116..51379193,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1026994	1.00[ASN][1000 genomes]
rs10747603	1.00[ASN][1000 genomes]
rs10783411	1.00[ASN][1000 genomes]
rs10783412	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10876126	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095997	0.95[AMR][1000 genomes]
rs11169679	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169718	1.00[JPT][hapmap]
rs11169724	1.00[JPT][hapmap]
rs12369066	1.00[JPT][hapmap]
rs12423207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs150909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161046	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125367	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17125370	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs17125416	1.00[JPT][hapmap]
rs17125418	1.00[JPT][hapmap]
rs17125428	1.00[JPT][hapmap]
rs17229232	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs2029147	1.00[ASN][1000 genomes]
rs2046498	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs224564	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224569	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.95[AFR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs224592	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224593	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554858	0.86[AMR][1000 genomes]
rs2554859	0.90[AMR][1000 genomes]
rs2554861	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630353	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630358	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2630366	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630367	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs319930	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs319938	1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs319940	0.82[EUR][1000 genomes]
rs319941	0.83[AMR][1000 genomes]
rs319943	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs319944	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs364627	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	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]
rs416062	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768959	0.89[ASW][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4768967	0.81[YRI][hapmap]
rs4768973	1.00[JPT][hapmap]
rs55874852	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][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[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	1.00[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6580783	0.89[ASW][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs686528	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs706804	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7138860	0.86[EUR][1000 genomes]
rs7299484	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960097	1.00[JPT][hapmap]
rs7969536	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.85[EUR][1000 genomes]
rs7971712	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[ASW][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975117	0.86[AMR][1000 genomes]
rs7975628	1.00[ASW][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs7978782	1.00[YRI][hapmap]
rs829016	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs829021	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs853236	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9739943	0.84[AFR][1000 genomes];0.80[AMR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2630362	SLC11A2	cis	lymphoblastoid	seeQTL
rs2630362	SLC11A2	cis	multi-tissue	Pritchard
rs2630362	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:51331800-51382000	Weak transcription	Ovary	ovary
3	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
4	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
5	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
6	chr12:51350800-51380600	Weak transcription	Fetal Lung	lung
7	chr12:51354400-51383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:51359800-51380400	Weak transcription	Fetal Kidney	kidney
9	chr12:51360200-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:51360600-51381000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:51360600-51381800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:51361600-51382200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:51362400-51378600	Weak transcription	NH-A	brain
14	chr12:51362400-51382000	Weak transcription	Lung	lung
15	chr12:51362800-51384400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:51363400-51384000	Weak transcription	Colonic Mucosa	Colon
17	chr12:51363600-51381200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:51364000-51380400	Weak transcription	K562	blood
19	chr12:51364600-51384400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:51366000-51378600	Weak transcription	HSMM	muscle
21	chr12:51366200-51380000	Weak transcription	Dnd41	blood
22	chr12:51366400-51379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:51366600-51380200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:51366800-51378600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:51366800-51382000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:51367000-51379600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:51367000-51380400	Weak transcription	Fetal Brain Female	brain
28	chr12:51367000-51380400	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:51367000-51382000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:51367200-51379800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:51367200-51382000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:51367200-51382000	Weak transcription	Fetal Stomach	stomach
33	chr12:51367200-51382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:51367400-51381800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:51371600-51380600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:51372200-51384600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:51373000-51381000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:51373400-51378800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:51373400-51383400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:51373800-51380200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:51374000-51378800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:51374000-51380600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:51374000-51381400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:51374200-51382000	Weak transcription	Pancreas	Pancrea
45	chr12:51374800-51378600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:51374800-51380200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr12:51375000-51379000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:51375000-51379200	Weak transcription	GM12878-XiMat	blood
49	chr12:51375000-51380400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr12:51375400-51380400	Weak transcription	Placenta	Placenta

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