Variant report

Variant	rs41296093
Chromosome Location	chr9:108156077-108156078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108154477..108157251-chr9:108163904..108166512,2	MCF-7	breast:
2	chr9:108153124..108158591-chr9:108160157..108165830,7	MCF-7	breast:
3	chr9:108150925..108153260-chr9:108154410..108158072,4	K562	blood:
4	chr9:108148770..108151493-chr9:108155727..108157351,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10491810	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991639	1.00[ASN][1000 genomes]
rs12339823	1.00[ASN][1000 genomes]
rs12340765	1.00[ASN][1000 genomes]
rs12342542	1.00[ASN][1000 genomes]
rs12344130	1.00[ASN][1000 genomes]
rs13294525	1.00[ASN][1000 genomes]
rs13294539	1.00[ASN][1000 genomes]
rs1410837	1.00[ASN][1000 genomes]
rs1410839	1.00[ASN][1000 genomes]
rs1553870	1.00[ASN][1000 genomes]
rs1553873	1.00[ASN][1000 genomes]
rs16924529	1.00[ASN][1000 genomes]
rs16924530	1.00[ASN][1000 genomes]
rs17246524	1.00[ASN][1000 genomes]
rs17305886	1.00[ASN][1000 genomes]
rs17305963	1.00[ASN][1000 genomes]
rs2771031	1.00[ASN][1000 genomes]
rs2771033	1.00[ASN][1000 genomes]
rs2771040	1.00[ASN][1000 genomes]
rs2812314	1.00[ASN][1000 genomes]
rs2812316	1.00[ASN][1000 genomes]
rs3199966	1.00[ASN][1000 genomes]
rs35603631	1.00[ASN][1000 genomes]
rs6479311	1.00[ASN][1000 genomes]
rs7024985	1.00[ASN][1000 genomes]
rs7045091	1.00[ASN][1000 genomes]
rs724069	1.00[ASN][1000 genomes]
rs7858401	1.00[ASN][1000 genomes]
rs907230	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	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41296093	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:108121600-108157000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:108125000-108166800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:108125600-108157000	Weak transcription	Osteobl	bone
5	chr9:108137800-108156200	Weak transcription	Fetal Stomach	stomach
6	chr9:108137800-108156400	Weak transcription	Aorta	Aorta
7	chr9:108137800-108157200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:108137800-108158200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:108138000-108156400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:108138000-108156400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:108143600-108157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:108146800-108177600	Weak transcription	Left Ventricle	heart
13	chr9:108148200-108156200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:108148200-108158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:108148200-108158800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:108148200-108160200	Weak transcription	Ovary	ovary
17	chr9:108148400-108156200	Weak transcription	Primary T cells from cord blood	blood
18	chr9:108148400-108156600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:108148400-108158600	Weak transcription	Fetal Lung	lung
20	chr9:108148400-108160400	Weak transcription	Fetal Intestine Large	intestine
21	chr9:108148400-108168000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:108148600-108158200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:108148800-108165600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:108150000-108156800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:108151800-108156800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:108152200-108157200	Enhancers	Brain Hippocampus Middle	brain
27	chr9:108152400-108156800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:108152600-108157000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:108152600-108157600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr9:108152600-108166000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:108152800-108159200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:108153200-108156800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:108153600-108163800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:108153600-108163800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:108154000-108156800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr9:108154400-108156600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr9:108155000-108164200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:108155200-108157000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:108155400-108156400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr9:108155400-108156400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:108155400-108156400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:108155400-108157200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr9:108155400-108158600	Weak transcription	Brain Angular Gyrus	brain
44	chr9:108155400-108158600	Weak transcription	Brain Substantia Nigra	brain
45	chr9:108155400-108172600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr9:108155600-108157000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:108155600-108158800	Weak transcription	Fetal Brain Female	brain
48	chr9:108155600-108164200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:108155600-108165600	Weak transcription	Brain Anterior Caudate	brain
50	chr9:108155800-108156200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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