Variant report

Variant	rs10122128
Chromosome Location	chr9:102693089-102693090
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	chr9:102668724..102670876-chr9:102691785..102694126,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255145	Chromatin interaction
ENSG00000136874	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10117638	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117828	0.93[ASN][1000 genomes]
rs10120103	0.93[ASN][1000 genomes]
rs10121601	0.92[ASN][1000 genomes]
rs10121880	0.93[ASN][1000 genomes]
rs10123261	0.93[ASN][1000 genomes]
rs10124366	0.81[ASN][1000 genomes]
rs10125981	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217337	0.93[ASN][1000 genomes]
rs10217366	0.93[ASN][1000 genomes]
rs10217692	0.93[ASN][1000 genomes]
rs10512268	0.93[ASN][1000 genomes]
rs1055187	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739791	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739793	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739794	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760698	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760699	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760700	0.93[ASN][1000 genomes]
rs10760704	0.93[ASN][1000 genomes]
rs10760705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760706	0.93[ASN][1000 genomes]
rs10819705	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819706	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819707	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819711	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819712	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988919	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988920	0.92[ASN][1000 genomes]
rs12352899	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830454	0.93[ASN][1000 genomes]
rs1852863	0.93[ASN][1000 genomes]
rs1881751	0.90[ASN][1000 genomes]
rs1962051	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997367	0.93[ASN][1000 genomes]
rs1997368	0.93[ASN][1000 genomes]
rs2031035	0.93[ASN][1000 genomes]
rs2416935	0.93[ASN][1000 genomes]
rs2416936	0.85[ASN][1000 genomes]
rs2416937	0.93[ASN][1000 genomes]
rs2416938	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416940	0.93[ASN][1000 genomes]
rs2416941	0.93[ASN][1000 genomes]
rs2416942	0.93[ASN][1000 genomes]
rs2900224	0.92[ASN][1000 genomes]
rs3739794	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3983846	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282626	0.93[ASN][1000 genomes]
rs4452862	0.93[ASN][1000 genomes]
rs4585797	0.93[ASN][1000 genomes]
rs4742777	0.93[ASN][1000 genomes]
rs4742778	0.93[ASN][1000 genomes]
rs4743370	0.93[ASN][1000 genomes]
rs6478987	0.93[ASN][1000 genomes]
rs6478988	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478990	0.93[ASN][1000 genomes]
rs7022208	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022999	0.93[ASN][1000 genomes]
rs7027619	0.93[ASN][1000 genomes]
rs7027813	0.95[ASN][1000 genomes]
rs7030388	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038506	0.93[ASN][1000 genomes]
rs7039716	0.93[ASN][1000 genomes]
rs7853264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299335	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1050510	chr9:102684318-102748658	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10122128	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
2	chr9:102671200-102719200	Weak transcription	Fetal Heart	heart
3	chr9:102680000-102710800	Weak transcription	HUVEC	blood vessel
4	chr9:102680400-102693800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:102680400-102724800	Weak transcription	HSMM	muscle
6	chr9:102682600-102693800	Weak transcription	Osteobl	bone
7	chr9:102682600-102751400	Weak transcription	NH-A	brain
8	chr9:102682800-102695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:102684400-102720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:102684600-102693600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:102685000-102698200	Weak transcription	NHEK	skin
12	chr9:102685000-102710000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr9:102685000-102731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:102685200-102730200	Weak transcription	NHLF	lung
15	chr9:102685800-102698000	Weak transcription	HMEC	breast
16	chr9:102686000-102695400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:102686000-102699400	Weak transcription	K562	blood
18	chr9:102686200-102694400	Weak transcription	Brain Substantia Nigra	brain
19	chr9:102686200-102699200	Weak transcription	Fetal Kidney	kidney
20	chr9:102686200-102699400	Weak transcription	Psoas Muscle	Psoas
21	chr9:102686200-102730000	Weak transcription	Colonic Mucosa	Colon
22	chr9:102686400-102693600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:102686400-102694600	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:102686400-102694600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:102686400-102699400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:102686400-102712800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:102686400-102713000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:102686400-102723400	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:102686400-102750800	Weak transcription	Esophagus	oesophagus
30	chr9:102686600-102693200	Weak transcription	Pancreas	Pancrea
31	chr9:102686600-102693800	Weak transcription	Right Ventricle	heart
32	chr9:102686600-102693800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:102686600-102694000	Weak transcription	Placenta	Placenta
34	chr9:102686600-102697200	Weak transcription	Thymus	Thymus
35	chr9:102686600-102698000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:102686600-102700200	Weak transcription	Aorta	Aorta
37	chr9:102686600-102713400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:102686600-102730800	Weak transcription	Ovary	ovary
39	chr9:102686600-102750800	Weak transcription	Gastric	stomach
40	chr9:102686800-102722800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:102687200-102698600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr9:102687800-102722200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr9:102688200-102698000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr9:102688200-102699400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:102688200-102713400	Weak transcription	Dnd41	blood
46	chr9:102688400-102693600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr9:102688400-102710800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:102689400-102693600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr9:102689400-102694400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:102689400-102696800	Weak transcription	Fetal Muscle Leg	muscle

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