Variant report

Variant	rs2416938
Chromosome Location	chr9:102680695-102680696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102581421..102582923-chr9:102680003..102681747,2	MCF-7	breast:
2	chr9:102679510..102681495-chr9:102684223..102687108,2	K562	blood:
3	chr9:102679685..102682942-chr9:102684269..102688000,3	K562	blood:
4	chr9:102668020..102670341-chr9:102679527..102681124,2	MCF-7	breast:
5	chr9:102668908..102670429-chr9:102679141..102681876,2	MCF-7	breast:
6	chr9:102674290..102678149-chr9:102678845..102681918,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237461	Chromatin interaction
ENSG00000136874	Chromatin interaction
ENSG00000255145	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10116142	0.84[JPT][hapmap]
rs10117638	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117828	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs10120103	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs10121601	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.92[ASN][1000 genomes]
rs10121880	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs10122128	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123261	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs10124366	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10125981	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217337	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs10217366	0.93[ASN][1000 genomes]
rs10217692	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs10512268	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs1055187	0.90[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739791	0.88[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739792	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739793	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739794	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760698	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760699	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760700	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760704	1.00[CHB][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs10760705	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760706	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs10819705	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819706	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819707	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819711	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819712	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988919	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988920	0.92[ASN][1000 genomes]
rs12352899	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918878	0.83[JPT][hapmap]
rs1830454	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.93[ASN][1000 genomes]
rs1852863	0.94[CHB][hapmap];0.83[YRI][hapmap];0.93[ASN][1000 genomes]
rs1881751	0.90[ASN][1000 genomes]
rs1962051	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969577	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997367	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs1997368	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs2031035	0.94[CHB][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs2416935	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs2416936	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs2416937	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs2416940	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs2416941	0.93[ASN][1000 genomes]
rs2416942	0.93[ASN][1000 genomes]
rs2900224	0.92[ASN][1000 genomes]
rs3739794	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3983846	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282626	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs4452862	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs4585797	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs4742777	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs4742778	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[ASN][1000 genomes]
rs4743370	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs6478987	0.93[ASN][1000 genomes]
rs6478988	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478990	0.93[ASN][1000 genomes]
rs7022208	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022999	0.93[ASN][1000 genomes]
rs7027619	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs7027813	0.95[ASN][1000 genomes]
rs7030388	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038506	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7039716	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.93[ASN][1000 genomes]
rs7853264	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299335	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs9556	0.83[JPT][hapmap]

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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2416938	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669600-102681200	Weak transcription	Spleen	Spleen
2	chr9:102669800-102681200	Weak transcription	Colonic Mucosa	Colon
3	chr9:102669800-102682400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:102669800-102684600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:102669800-102684800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:102669800-102686000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:102669800-102686200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:102669800-102687600	Weak transcription	Stomach Mucosa	stomach
9	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
10	chr9:102670000-102680800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:102670000-102684400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:102670000-102684400	Weak transcription	HSMMtube	muscle
13	chr9:102670000-102686000	Weak transcription	Psoas Muscle	Psoas
14	chr9:102670000-102688200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:102670400-102681000	Weak transcription	Osteobl	bone
16	chr9:102670400-102681600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:102670400-102686000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:102670400-102688600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:102671200-102681200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:102671200-102719200	Weak transcription	Fetal Heart	heart
21	chr9:102676400-102681000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr9:102676400-102681600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:102676400-102684600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:102676600-102682200	Strong transcription	Fetal Lung	lung
25	chr9:102676600-102684800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr9:102676600-102688000	Strong transcription	Primary B cells from cord blood	blood
27	chr9:102676800-102681600	Strong transcription	Primary hematopoietic stem cells	blood
28	chr9:102677200-102680800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:102677400-102681600	Strong transcription	Primary T cells from cord blood	blood
30	chr9:102677400-102682600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:102677400-102685600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:102677400-102686600	Strong transcription	Placenta	Placenta
33	chr9:102677400-102686600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr9:102677600-102680800	Strong transcription	NH-A	brain
35	chr9:102677600-102681200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr9:102677600-102681600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:102677600-102681600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:102677600-102681600	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr9:102677600-102681800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr9:102677600-102682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:102677600-102682000	Strong transcription	Adipose Nuclei	Adipose
42	chr9:102677600-102682400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr9:102677600-102682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:102677600-102682800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:102677600-102683200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:102677600-102684800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:102677600-102685200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:102677600-102685800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:102677600-102686000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr9:102677600-102686400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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