Variant report

Variant	rs7858401
Chromosome Location	chr9:108109636-108109637
allele	C/T
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:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

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	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs12344130	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12378850	1.00[CHD][hapmap]
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	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553873	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924529	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924530	0.80[CEU][hapmap];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	0.80[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs35603631	1.00[ASN][1000 genomes]
rs41296093	1.00[ASN][1000 genomes]
rs4387039	1.00[CHD][hapmap]
rs6479311	1.00[ASN][1000 genomes]
rs7024985	1.00[ASN][1000 genomes]
rs7044901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7045091	1.00[ASN][1000 genomes]
rs724069	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
rs7858401	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 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	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:108092000-108124000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
6	chr9:108093200-108123200	Weak transcription	Colonic Mucosa	Colon
7	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
8	chr9:108095600-108122200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:108096400-108131800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr9:108097000-108122800	Weak transcription	Fetal Kidney	kidney
12	chr9:108097200-108124600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:108097400-108133600	Weak transcription	Placenta	Placenta
14	chr9:108097600-108147000	Weak transcription	HMEC	breast
15	chr9:108099200-108122200	Weak transcription	Lung	lung
16	chr9:108099200-108123400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:108099200-108123800	Weak transcription	Aorta	Aorta
18	chr9:108099600-108122200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:108100000-108117200	Weak transcription	Fetal Lung	lung
20	chr9:108100200-108111200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:108100200-108112000	Weak transcription	Primary T cells from cord blood	blood
22	chr9:108100200-108115000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:108100200-108123000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:108100200-108123400	Weak transcription	Fetal Stomach	stomach
25	chr9:108100200-108136200	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
27	chr9:108100400-108112000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:108100400-108115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:108100400-108122200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:108100600-108112800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:108100600-108123400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr9:108101000-108110200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr9:108101000-108110600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:108101000-108121600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:108101000-108122200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:108102000-108112000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:108102200-108111400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:108104800-108120200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:108104800-108122800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr9:108104800-108124000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:108104800-108124200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:108104800-108129600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:108104800-108147600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:108105000-108111400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:108105000-108112000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:108105000-108112000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:108105000-108112000	Weak transcription	Left Ventricle	heart
48	chr9:108105000-108122200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:108105000-108122200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:108105000-108122400	Weak transcription	HSMM	muscle

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