Variant report

Variant	rs2417615
Chromosome Location	chr9:108087851-108087852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108087480..108089779-chr9:108111023..108113317,2	K562	blood:
2	chr9:108080682..108083667-chr9:108087313..108089895,3	MCF-7	breast:
3	chr9:108086313..108088804-chr9:108089116..108090830,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10123494	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10820801	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10991629	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991639	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12339823	0.81[AMR][1000 genomes]
rs12342542	0.81[AMR][1000 genomes]
rs12350138	0.92[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13294525	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13294539	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1410839	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16924530	0.83[AMR][1000 genomes]
rs2771033	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2771040	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3199966	0.81[AMR][1000 genomes]
rs34659648	1.00[ASN][1000 genomes]
rs34750132	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35603631	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4549843	0.84[CEU][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479311	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6479313	0.92[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479314	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479315	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479316	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7019052	1.00[ASN][1000 genomes]
rs7024985	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7029443	1.00[CEU][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7045091	1.00[CEU][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7865985	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907230	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][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
rs2417615	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108054600-108090800	Weak transcription	Psoas Muscle	Psoas
2	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
3	chr9:108062200-108091400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:108062200-108091800	Weak transcription	Aorta	Aorta
5	chr9:108062200-108098800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr9:108062400-108098800	Weak transcription	Spleen	Spleen
7	chr9:108062400-108104600	Weak transcription	Right Ventricle	heart
8	chr9:108062600-108090800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:108062600-108090800	Weak transcription	Fetal Thymus	thymus
10	chr9:108062600-108091000	Weak transcription	Adipose Nuclei	Adipose
11	chr9:108062600-108091600	Weak transcription	NHDF-Ad	bronchial
12	chr9:108062600-108098600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr9:108062600-108098800	Weak transcription	Left Ventricle	heart
14	chr9:108062600-108098800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:108062800-108098400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr9:108062800-108098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:108066200-108098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:108068800-108098600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:108069000-108104000	Weak transcription	Fetal Heart	heart
20	chr9:108070400-108091800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:108070400-108093400	Weak transcription	Gastric	stomach
22	chr9:108070400-108094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:108071400-108090400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:108071600-108099000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:108071800-108097800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:108072200-108090200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:108072200-108090400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:108072400-108094200	Weak transcription	HSMM	muscle
29	chr9:108072400-108098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:108072600-108091400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr9:108072600-108094800	Weak transcription	HSMMtube	muscle
32	chr9:108076000-108096200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:108076600-108089800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:108077200-108090800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:108078400-108101800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:108079600-108098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:108080000-108098800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:108080400-108097800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:108081000-108123000	Weak transcription	Primary B cells from cord blood	blood
40	chr9:108081600-108090600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:108081600-108091600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:108081600-108096400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr9:108081800-108090400	Weak transcription	Brain Angular Gyrus	brain
44	chr9:108081800-108091800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:108082000-108090000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:108082000-108090600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:108082000-108091800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr9:108082000-108097600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr9:108082000-108098800	Weak transcription	Pancreas	Pancrea
50	chr9:108082200-108098600	Weak transcription	Primary T cells from cord blood	blood

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