Variant report

Variant	rs10217329
Chromosome Location	chr9:100004511-100004512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100003140..100004870-chr9:100029614..100032184,2	K562	blood:
2	chr9:99999075..100002333-chr9:100004185..100008617,4	K562	blood:
3	chr9:99999075..100001905-chr9:100002725..100008617,7	K562	blood:

Variant related genes	Relation type
ENSG00000203279	Chromatin interaction
ENSG00000254876	Chromatin interaction
ENSG00000254483	Chromatin interaction
ENSG00000197816	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10115798	0.91[EUR][1000 genomes]
rs10116404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217229	0.88[EUR][1000 genomes]
rs10435866	0.81[EUR][1000 genomes]
rs10733584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733603	0.81[EUR][1000 genomes]
rs10739337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739365	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759605	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759610	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759619	0.82[EUR][1000 genomes]
rs10817300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817361	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817403	0.86[ASN][1000 genomes]
rs10817448	0.83[EUR][1000 genomes]
rs10981362	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981528	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981537	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981551	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981557	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981560	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981625	0.84[EUR][1000 genomes]
rs12683119	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12683933	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1462086	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1462087	0.83[EUR][1000 genomes]
rs1462092	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1531439	0.80[AMR][1000 genomes]
rs1857084	0.85[ASN][1000 genomes]
rs1870859	0.84[EUR][1000 genomes]
rs1935372	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061634	0.83[EUR][1000 genomes]
rs2061635	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2255135	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255139	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255244	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2401382	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447287	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447288	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447289	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447290	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487874	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487875	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2502646	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2615144	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795363	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795366	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795369	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795370	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818236	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818237	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818240	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818241	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818242	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818244	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859564	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888960	0.89[EUR][1000 genomes]
rs3953688	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994559	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994561	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994562	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4345679	0.84[EUR][1000 genomes]
rs4433262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4437755	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4507886	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4524907	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4615708	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4645658	0.83[EUR][1000 genomes]
rs4742683	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4742684	0.83[EUR][1000 genomes]
rs4743067	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743074	0.84[EUR][1000 genomes]
rs4743075	0.83[EUR][1000 genomes]
rs6477982	0.85[ASN][1000 genomes]
rs6477988	0.85[ASN][1000 genomes]
rs6477993	0.85[ASN][1000 genomes]
rs6478008	0.84[AMR][1000 genomes]
rs6478043	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478044	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478048	0.88[EUR][1000 genomes]
rs6478051	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478054	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478055	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478059	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7020002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020144	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021895	0.84[AMR][1000 genomes]
rs7023087	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026287	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026893	0.83[EUR][1000 genomes]
rs7029749	0.81[EUR][1000 genomes]
rs7033212	0.92[EUR][1000 genomes]
rs7033480	0.85[EUR][1000 genomes]
rs7033642	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7036964	0.82[EUR][1000 genomes]
rs7038353	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047367	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71491754	0.86[EUR][1000 genomes]
rs725228	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725229	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs752243	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7847332	0.81[EUR][1000 genomes]
rs7850473	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7855385	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855956	0.82[EUR][1000 genomes]
rs7860264	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867330	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7868052	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868295	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868312	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7875158	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7875296	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9299202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9408859	0.88[EUR][1000 genomes]
rs9409139	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10217329	CCDC180	cis	Artery Tibial	GTEx
rs10217329	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs10217329	RP11-23J9.4	cis	Artery Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100001200-100011000	Weak transcription	Lung	lung
2	chr9:100001200-100017000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:100001200-100039400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:100001400-100005800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:100001400-100010800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:100001400-100014000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr9:100001400-100017600	Weak transcription	Left Ventricle	heart
8	chr9:100001400-100017800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:100001600-100005800	Weak transcription	NHEK	skin
10	chr9:100001600-100012800	Weak transcription	Fetal Kidney	kidney
11	chr9:100001600-100014000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:100001600-100022200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:100001600-100037400	Weak transcription	Primary T cells from cord blood	blood
14	chr9:100001800-100004600	Weak transcription	Fetal Lung	lung
15	chr9:100001800-100005600	Weak transcription	Osteobl	bone
16	chr9:100001800-100005800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:100001800-100012800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr9:100002000-100005000	Weak transcription	Brain Anterior Caudate	brain
19	chr9:100002000-100005600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:100002000-100005800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:100002000-100010400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:100002000-100011000	Weak transcription	Fetal Stomach	stomach
23	chr9:100002000-100011600	Weak transcription	Pancreas	Pancrea
24	chr9:100002000-100013200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:100002000-100013400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:100002000-100015200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:100002000-100016600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:100002000-100016600	Weak transcription	Thymus	Thymus
29	chr9:100002000-100018000	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:100002000-100023000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:100002000-100025400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:100002000-100037400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:100002000-100037800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:100002000-100038600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:100002000-100038600	Weak transcription	Fetal Intestine Large	intestine
36	chr9:100002000-100038600	Weak transcription	Fetal Intestine Small	intestine
37	chr9:100002000-100038800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr9:100002000-100038800	Weak transcription	Ovary	ovary
39	chr9:100002000-100038800	Weak transcription	Right Ventricle	heart
40	chr9:100002000-100039000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:100002000-100039600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr9:100002000-100039600	Weak transcription	Adipose Nuclei	Adipose
43	chr9:100002000-100039600	Weak transcription	Colon Smooth Muscle	Colon
44	chr9:100002000-100039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:100002000-100040400	Weak transcription	Spleen	Spleen
46	chr9:100002200-100010800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:100002200-100013000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:100002200-100014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:100002200-100038800	Weak transcription	Liver	Liver
50	chr9:100002200-100039400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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