Variant report

Variant	rs1553873
Chromosome Location	chr9:108105253-108105254
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108104206..108106322-chr9:108107327..108109890,2	MCF-7	breast:
2	chr9:108049663..108051897-chr9:108104930..108106887,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10491810	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[CEU][hapmap];0.81[EUR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924529	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];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]
rs41296093	1.00[ASN][1000 genomes]
rs6479311	1.00[ASN][1000 genomes]
rs7024985	1.00[ASN][1000 genomes]
rs7044901	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7045091	1.00[ASN][1000 genomes]
rs724069	1.00[ASN][1000 genomes]
rs7858401	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907230	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	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
rs1553873	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108081000-108123000	Weak transcription	Primary B cells from cord blood	blood
3	chr9:108090800-108108600	Weak transcription	Brain Germinal Matrix	brain
4	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:108092000-108124000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
7	chr9:108093200-108108400	Weak transcription	Fetal Brain Female	brain
8	chr9:108093200-108123200	Weak transcription	Colonic Mucosa	Colon
9	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
10	chr9:108095600-108122200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:108096400-108131800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr9:108097000-108122800	Weak transcription	Fetal Kidney	kidney
14	chr9:108097200-108124600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:108097400-108133600	Weak transcription	Placenta	Placenta
16	chr9:108097600-108147000	Weak transcription	HMEC	breast
17	chr9:108097800-108108400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:108099200-108122200	Weak transcription	Lung	lung
19	chr9:108099200-108123400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:108099200-108123800	Weak transcription	Aorta	Aorta
21	chr9:108099600-108108200	Weak transcription	HepG2	liver
22	chr9:108099600-108122200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:108100000-108117200	Weak transcription	Fetal Lung	lung
24	chr9:108100200-108111200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:108100200-108112000	Weak transcription	Primary T cells from cord blood	blood
26	chr9:108100200-108115000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:108100200-108123000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:108100200-108123400	Weak transcription	Fetal Stomach	stomach
29	chr9:108100200-108136200	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
31	chr9:108100400-108112000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:108100400-108115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:108100400-108122200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:108100600-108112800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:108100600-108123400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:108101000-108108400	Weak transcription	Fetal Intestine Large	intestine
37	chr9:108101000-108110200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:108101000-108110600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:108101000-108121600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:108101000-108122200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:108102000-108112000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:108102200-108111400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:108102400-108105800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:108102600-108106600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:108104600-108106600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:108104600-108106600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr9:108104800-108106000	Enhancers	Brain Hippocampus Middle	brain
48	chr9:108104800-108107600	Weak transcription	Brain Anterior Caudate	brain
49	chr9:108104800-108108600	Weak transcription	Fetal Heart	heart
50	chr9:108104800-108108600	Weak transcription	Stomach Mucosa	stomach

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