Variant report

Variant	rs7029408
Chromosome Location	chr9:115963782-115963783
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115955703..115958661-chr9:115961003..115965387,3	MCF-7	breast:
2	chr9:115963672..115965977-chr9:115972388..115974143,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10081639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10081701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10114293	0.94[AFR][1000 genomes]
rs10117100	0.92[AFR][1000 genomes]
rs10118429	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121981	0.90[ASN][1000 genomes]
rs10122151	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10123301	0.94[AFR][1000 genomes]
rs10817454	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981662	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981679	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981687	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1128786	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1133619	0.94[AFR][1000 genomes]
rs1133620	0.94[AFR][1000 genomes]
rs12236187	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346816	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684417	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910202	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17762642	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28574672	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28790397	0.94[AFR][1000 genomes]
rs28790632	0.94[AFR][1000 genomes]
rs28830537	0.92[AFR][1000 genomes]
rs28891677	0.92[AFR][1000 genomes]
rs3810910	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3934969	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4378033	0.94[AFR][1000 genomes]
rs4407968	0.94[AFR][1000 genomes]
rs4490910	0.94[AFR][1000 genomes]
rs5015972	0.89[AFR][1000 genomes]
rs68122369	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7021999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029139	0.94[AFR][1000 genomes]
rs7029228	0.94[AFR][1000 genomes]
rs7029472	0.94[AFR][1000 genomes]
rs7030027	0.94[AFR][1000 genomes]
rs7033282	0.94[AFR][1000 genomes]
rs7034425	0.94[AFR][1000 genomes]
rs7038133	0.94[AFR][1000 genomes]
rs7038260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758243	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73550301	0.94[AFR][1000 genomes]
rs73655844	0.94[AFR][1000 genomes]
rs73655845	0.93[AFR][1000 genomes]
rs7849150	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7850672	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850723	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851935	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852613	0.94[AFR][1000 genomes]
rs7854882	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7855105	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7856067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860472	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863351	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7865125	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7865445	0.94[AFR][1000 genomes]
rs7865584	0.92[AFR][1000 genomes]
rs7865650	0.94[AFR][1000 genomes]
rs7866432	0.94[AFR][1000 genomes]
rs7874583	0.94[AFR][1000 genomes]
rs9695716	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9722731	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7029408	SLC31A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115920000-115970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:115920000-115973400	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr9:115920400-115973400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:115920800-115966400	Strong transcription	Dnd41	blood
5	chr9:115920800-115975000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:115923400-115976400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr9:115924000-115965800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:115924200-115969600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:115927600-115973400	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr9:115936800-115982400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:115941200-115968600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr9:115941200-115969200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:115945400-115977200	Weak transcription	Stomach Mucosa	stomach
14	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:115950400-115972800	Weak transcription	Right Ventricle	heart
16	chr9:115950600-115968600	Weak transcription	Fetal Heart	heart
17	chr9:115950600-115982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:115951000-115972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:115951000-115972200	Weak transcription	Gastric	stomach
21	chr9:115951000-115972200	Weak transcription	Pancreas	Pancrea
22	chr9:115951000-115974000	Strong transcription	Placenta	Placenta
23	chr9:115951000-115982800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:115951200-115964800	Weak transcription	Fetal Brain Male	brain
25	chr9:115951400-115967800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:115952200-115968000	Strong transcription	GM12878-XiMat	blood
27	chr9:115952200-115974400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:115952400-115965800	Strong transcription	Primary T cells from cord blood	blood
29	chr9:115952400-115973400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:115952400-115973600	Strong transcription	Adipose Nuclei	Adipose
31	chr9:115952400-115974400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:115953400-115967200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr9:115953600-115967600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr9:115954000-115965400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:115954600-115965200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr9:115954600-115973600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:115956000-115973400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:115956200-115971800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr9:115956600-115964000	Weak transcription	Fetal Brain Female	brain
40	chr9:115956600-115968800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:115956600-115972200	Weak transcription	Aorta	Aorta
42	chr9:115956600-115972200	Weak transcription	Esophagus	oesophagus
43	chr9:115957200-115966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr9:115957400-115965400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr9:115957400-115970000	Strong transcription	HUVEC	blood vessel
46	chr9:115957600-115967200	Strong transcription	Primary B cells from cord blood	blood
47	chr9:115957600-115972000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:115957600-115974000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr9:115957800-115965400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:115957800-115970800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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