Variant report

Variant	rs10981662
Chromosome Location	chr9:115929962-115929963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115910740..115913540-chr9:115929210..115931968,2	K562	blood:
2	chr9:115928135..115929979-chr9:115931425..115934458,3	MCF-7	breast:
3	chr9:115924412..115926824-chr9:115928011..115930786,2	MCF-7	breast:
4	chr9:115929834..115932137-chr9:115938047..115940360,2	MCF-7	breast:
5	chr9:115910740..115914842-chr9:115929210..115933817,4	K562	blood:
6	chr9:115929480..115931440-chr9:115950780..115952442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119321	Chromatin interaction
ENSG00000136867	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10081639	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10081701	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10118429	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10121981	0.96[ASN][1000 genomes]
rs10122151	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817454	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981679	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981682	0.88[AFR][1000 genomes]
rs10981686	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10981687	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1128786	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133618	0.88[AFR][1000 genomes]
rs12236187	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12346816	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12684417	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910202	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17762642	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28574672	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28887481	0.86[AFR][1000 genomes]
rs3810910	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934969	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4333682	0.88[AFR][1000 genomes]
rs4548256	0.83[AFR][1000 genomes]
rs68122369	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7021999	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7029408	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7038260	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72758243	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7467537	0.85[ASN][1000 genomes]
rs7849150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7850672	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850723	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7851935	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7854882	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7855105	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7856067	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7860472	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7863351	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7865125	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9695716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv1051654	chr9:115881588-115935663	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv466507	chr9:115905850-115936903	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv615213	chr9:115905850-115936903	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10981662	SLC31A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115915200-115930200	Weak transcription	Stomach Mucosa	stomach
2	chr9:115917800-115949400	Strong transcription	Placenta	Placenta
3	chr9:115918400-115947200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:115918600-115930200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:115918800-115937000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:115919000-115935600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:115919000-115936800	Strong transcription	Fetal Brain Female	brain
8	chr9:115919200-115937400	Strong transcription	HMEC	breast
9	chr9:115919200-115950800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:115919400-115936800	Strong transcription	Pancreas	Pancrea
11	chr9:115919400-115937000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:115919400-115937200	Strong transcription	Fetal Stomach	stomach
13	chr9:115919400-115950800	Strong transcription	Primary T cells from cord blood	blood
14	chr9:115919400-115954200	Strong transcription	Fetal Intestine Large	intestine
15	chr9:115919600-115936800	Strong transcription	Fetal Intestine Small	intestine
16	chr9:115919600-115938000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:115919600-115938800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr9:115919600-115940200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:115919800-115937000	Strong transcription	Fetal Muscle Leg	muscle
20	chr9:115919800-115939400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr9:115920000-115939000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr9:115920000-115942400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr9:115920000-115950200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:115920000-115951400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:115920000-115970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:115920000-115973400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr9:115920200-115956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:115920400-115937200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:115920400-115973400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr9:115920600-115937200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:115920600-115941600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr9:115920800-115966400	Strong transcription	Dnd41	blood
33	chr9:115920800-115975000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:115921000-115937800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:115921200-115930000	Genic enhancers	Brain Substantia Nigra	brain
36	chr9:115921200-115936800	Strong transcription	Thymus	Thymus
37	chr9:115921800-115936800	Strong transcription	Primary B cells from cord blood	blood
38	chr9:115921800-115951000	Strong transcription	Fetal Thymus	thymus
39	chr9:115922400-115942000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:115922800-115956400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr9:115923000-115942200	Strong transcription	GM12878-XiMat	blood
42	chr9:115923000-115956200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:115923200-115937000	Strong transcription	Lung	lung
44	chr9:115923200-115940800	Strong transcription	NHEK	skin
45	chr9:115923400-115934000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:115923400-115934000	Strong transcription	Hela-S3	cervix
47	chr9:115923400-115941800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:115923400-115976400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr9:115923600-115934000	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr9:115923600-115937000	Strong transcription	Colonic Mucosa	Colon

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