Variant report

Variant	rs10799311
Chromosome Location	chr1:225650626-225650627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225649550..225651644-chr1:225657315..225659303,2	MCF-7	breast:
2	chr1:225626720..225628379-chr1:225647904..225650755,2	K562	blood:
3	chr1:225648477..225651119-chr1:225966156..225969061,2	K562	blood:
4	chr1:225637801..225642696-chr1:225647950..225650939,4	K562	blood:
5	chr1:225646346..225648004-chr1:225649524..225651043,2	K562	blood:
6	chr1:225646305..225648757-chr1:225649524..225652760,3	K562	blood:
7	chr1:225615091..225616977-chr1:225649695..225651542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10753406	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799314	0.89[AMR][1000 genomes]
rs10799315	0.81[AMR][1000 genomes]
rs10799317	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799318	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10799319	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10915828	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10915830	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915833	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915834	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10915839	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10915847	0.88[EUR][1000 genomes]
rs11584675	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028305	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12729655	0.81[AMR][1000 genomes]
rs3820226	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3856156	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653637	0.86[ASN][1000 genomes]
rs4653639	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4653643	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs487591	0.83[EUR][1000 genomes]
rs498350	0.81[EUR][1000 genomes]
rs510293	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs511649	0.83[EUR][1000 genomes]
rs516249	0.85[EUR][1000 genomes]
rs551996	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs554744	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs554992	0.81[EUR][1000 genomes]
rs561656	0.81[EUR][1000 genomes]
rs576861	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426076	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6426077	0.82[ASN][1000 genomes]
rs6668770	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6697783	0.87[ASN][1000 genomes]
rs6702452	0.85[ASN][1000 genomes]
rs6702538	0.87[ASN][1000 genomes]
rs6702555	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6751	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs712062	0.83[EUR][1000 genomes]
rs7515907	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7515939	0.87[ASN][1000 genomes]
rs7524766	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7540181	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7541598	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7549456	0.85[ASN][1000 genomes]
rs7555139	0.88[EUR][1000 genomes]
rs7555553	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs947034	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9804142	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10799311	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225642400-225650800	Weak transcription	Right Atrium	heart
2	chr1:225642400-225653000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
4	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:225642800-225652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:225643000-225651000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:225647000-225651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:225647000-225651600	Enhancers	Fetal Muscle Leg	muscle
10	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
11	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
12	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:225647200-225651600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:225647400-225651200	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:225647600-225652000	Enhancers	Fetal Stomach	stomach
17	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:225647800-225653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:225648000-225651400	Enhancers	Fetal Brain Male	brain
20	chr1:225648000-225652600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:225648200-225651000	Weak transcription	Fetal Intestine Small	intestine
22	chr1:225648400-225653400	Weak transcription	Fetal Intestine Large	intestine
23	chr1:225648600-225650800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:225648600-225651000	Weak transcription	Gastric	stomach
25	chr1:225648600-225651200	Enhancers	Fetal Brain Female	brain
26	chr1:225648600-225652800	Weak transcription	Fetal Kidney	kidney
27	chr1:225648800-225650800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:225648800-225650800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:225648800-225650800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:225648800-225650800	Enhancers	Fetal Heart	heart
31	chr1:225648800-225651000	Weak transcription	HMEC	breast
32	chr1:225648800-225651400	Enhancers	Ovary	ovary
33	chr1:225648800-225652000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
34	chr1:225648800-225652200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:225648800-225652600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:225648800-225652600	Weak transcription	Osteobl	bone
37	chr1:225648800-225654600	Weak transcription	HUVEC	blood vessel
38	chr1:225649000-225652600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:225649000-225653200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:225649000-225654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:225649200-225650800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:225649200-225650800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:225649200-225650800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:225649200-225651000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:225649200-225652000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr1:225649200-225652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:225649200-225652800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:225649200-225654400	Weak transcription	Primary T cells from cord blood	blood
49	chr1:225649400-225650800	Weak transcription	Left Ventricle	heart
50	chr1:225649400-225653400	Weak transcription	Dnd41	blood

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