Variant report

Variant	rs9409550
Chromosome Location	chr9:97223294-97223295
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	chr9:25599854..25601775-chr9:97221816..97224638,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10821345	0.98[ASN][1000 genomes]
rs10821352	0.97[ASN][1000 genomes]
rs10993210	0.98[ASN][1000 genomes]
rs11789704	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12002028	0.96[ASN][1000 genomes]
rs12236578	0.90[ASN][1000 genomes]
rs16909983	0.94[ASN][1000 genomes]
rs16910109	0.94[ASN][1000 genomes]
rs1752784	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs2486632	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2769813	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2769816	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2993948	0.87[CEU][hapmap]
rs4612412	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744338	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4744345	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55877910	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs594198	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61628907	0.96[ASN][1000 genomes]
rs639276	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042481	0.87[CEU][hapmap]
rs7858082	0.88[CEU][hapmap]
rs9409546	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409564	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409565	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409567	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9409767	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409771	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409778	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409780	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409787	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv893593	chr9:97196979-97228918	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv893594	chr9:97221463-97283226	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9409550	HIATL1	cis	multi-tissue	Pritchard
rs9409550	HIATL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97201000-97223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:97201000-97224600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr9:97201000-97225000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:97201000-97225800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:97201400-97225200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:97201600-97224800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:97202000-97224200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:97202200-97225600	Strong transcription	Dnd41	blood
9	chr9:97203200-97225000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:97204400-97227000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:97206200-97225800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:97206600-97224400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:97206800-97225200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr9:97206800-97225600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:97207000-97225800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr9:97207200-97224800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:97208200-97224800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:97208400-97224600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:97208400-97225200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr9:97209000-97225000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:97209000-97225400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:97209200-97224200	Strong transcription	Liver	Liver
23	chr9:97209200-97225200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:97209200-97225600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:97209600-97223600	Strong transcription	Fetal Thymus	thymus
26	chr9:97209600-97224400	Strong transcription	Osteobl	bone
27	chr9:97209600-97224800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:97209800-97225200	Strong transcription	Placenta	Placenta
29	chr9:97209800-97225600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:97210000-97225200	Strong transcription	Fetal Muscle Leg	muscle
31	chr9:97211600-97224400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:97212400-97224800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:97212600-97225400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:97212600-97225400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:97213800-97224000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr9:97213800-97224800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr9:97214000-97224400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:97215200-97223800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:97215200-97225400	Strong transcription	Primary B cells from cord blood	blood
40	chr9:97215200-97225400	Strong transcription	Primary T cells from cord blood	blood
41	chr9:97215200-97225800	Strong transcription	HSMM	muscle
42	chr9:97215400-97225200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:97215400-97225400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:97215600-97224200	Strong transcription	Adipose Nuclei	Adipose
45	chr9:97215800-97225000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:97215800-97225000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr9:97215800-97225200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:97215800-97225200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr9:97215800-97225400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:97215800-97225600	Strong transcription	Duodenum Mucosa	Duodenum

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