Variant report

Variant	rs41269915
Chromosome Location	chr1:154521584-154521585
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154521533-154521888	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:154521579-154521797	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:154521096-154522544	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:154521484-154521706	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:154521287-154522233	GM12891	blood:	n/a	n/a
6	CTCF	chr1:154521540-154521690	GM12868	blood:	n/a	n/a
7	POLR2A	chr1:154521325-154521795	K562	blood:	n/a	n/a
8	POLR2A	chr1:154521488-154521612	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:154521522-154522119	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:154521458-154522055	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:154521547-154521916	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:154521516-154522035	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:154521471-154522133	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr1:154521582-154521797	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:154521573-154522406	K562	blood:	n/a	n/a
16	POLR2A	chr1:154521409-154522485	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:154521578-154521628	HEEpiC	esophagus:	n/a
2	chr1:154521578-154521628	NHDF-neo	bronchial:	n/a
3	chr1:154521578-154521628	NB4	blood:	n/a
4	chr1:154521578-154521628	CMK	blood:	n/a
5	chr1:154521578-154521628	HepG2	liver:	n/a
6	chr1:154521578-154521628	HIPEpiC	eye:	n/a
7	chr1:154521578-154521628	SK-N-SH_RA	brain:	n/a
8	chr1:154521578-154521628	HEK293	kidney:	embryo
9	chr1:154521578-154521628	HPAEpiC	pulmonary alveolar:	n/a
10	chr1:154521578-154521628	NHBE	bronchial:	n/a
11	chr1:154521578-154521628	HUVEC	blood vessel:	n/a
12	chr1:154521578-154521628	NT2-D1	testis:	n/a
13	chr1:154521578-154521628	HCPEpiC	choroid plexus:	n/a
14	chr1:154521578-154521628	RPTEC	kidney:	n/a
15	chr1:154521578-154521628	NH-A	brain:	n/a
16	chr1:154521578-154521628	ECC-1	luminal epithelium:	n/a
17	chr1:154521578-154521628	HRCEpiC	kidney:	n/a
18	chr1:154521578-154521628	Jurkat	blood:	n/a
19	chr1:154521578-154521628	K562	blood:	n/a
20	chr1:154521578-154521628	HCM	heart:	n/a
21	chr1:154521578-154521628	A549	lung:	n/a
22	chr1:154521578-154521628	AoSMC	blood vessel:	n/a
23	chr1:154521578-154521628	U87	brain:	n/a
24	chr1:154521578-154521628	HCF	heart:	n/a
25	chr1:154521578-154521628	ProgFib	skin:	n/a
26	chr1:154521578-154521628	HCT-116	colon:	n/a
27	chr1:154521578-154521628	SAEC	small airway:	n/a
28	chr1:154521578-154521628	Caco-2	colon:	n/a
29	chr1:154521578-154521628	GM12878	blood:	n/a
30	chr1:154521578-154521628	SK-N-MC	brain:	n/a
31	chr1:154521578-154521628	GM12892	blood:	n/a
32	chr1:154521578-154521628	BE2_C	brain:	n/a
33	chr1:154521578-154521628	H1-hESC	embryonic stem cell:	embryo
34	chr1:154521578-154521628	HNPCEpiC	eye:	n/a
35	chr1:154521578-154521628	GM19239	blood:	n/a
36	chr1:154521578-154521628	HRE	kidney:	n/a
37	chr1:154521578-154521628	MCF10A-Er-Src	breast:	n/a
38	chr1:154521578-154521628	ovcar-3	ovarian:	n/a
39	chr1:154521578-154521628	SK-N-SH	brain:	n/a
40	chr1:154521578-154521628	HL-60	blood:	n/a
41	chr1:154521578-154521628	PANC-1	pancreas:	n/a
42	chr1:154521578-154521628	AG10803	skin:	n/a
43	chr1:154521578-154521628	PrEC	prostate:	n/a
44	chr1:154521578-154521628	HRPEpiC	eye:	n/a
45	chr1:154521578-154521628	GM06990	blood:	n/a
46	chr1:154521578-154521628	SKMC	muscle:	n/a
47	chr1:154521578-154521628	AG09319	gingival:	n/a
48	chr1:154521578-154521628	T-47D	breast:	n/a
49	chr1:154521578-154521628	PFSK-1	brain:	n/a
50	chr1:154521578-154521628	AG09309	skin:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154514220..154517207-chr1:154519494..154521749,2	MCF-7	breast:
2	chr1:154521062..154522565-chr1:154552295..154555132,2	K562	blood:
3	chr1:154457195..154459578-chr1:154521193..154523267,2	MCF-7	breast:
4	chr1:154519911..154522029-chr1:154904733..154906266,2	MCF-7	breast:
5	chr1:154450895..154452551-chr1:154521385..154523555,2	K562	blood:
6	chr1:154450895..154452428-chr1:154521385..154523605,2	K562	blood:
7	chr1:154505752..154507416-chr1:154519791..154523033,3	MCF-7	breast:

No data

Variant related genes	Relation type
UBE2Q1-AS1	TF binding region
UBE2Q1-AS1	CpG island
ENSG00000163239	Chromatin interaction
ENSG00000273110	Chromatin interaction
ENSG00000169291	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10047079	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11490956	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12403537	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12405637	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12406822	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12408461	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2229238	0.87[EUR][1000 genomes]
rs3811448	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811449	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4072391	0.87[EUR][1000 genomes]
rs41308419	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41313910	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4379670	0.88[EUR][1000 genomes]
rs4390168	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4633282	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4639752	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57783436	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58348886	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58710275	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58881140	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59084843	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59239860	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59741504	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59838898	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60092776	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60255122	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60368585	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60498985	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60760897	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60931472	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61275241	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61403567	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61559765	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61698846	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6669229	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672087	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6674171	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681207	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72999415	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72999419	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72999422	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73018293	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73020232	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73020234	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73020246	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73023331	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73023339	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73023346	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73023348	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73023349	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514452	0.86[EUR][1000 genomes]
rs7526293	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7551873	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556449	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41269915	TDRD10	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154513600-154528400	Weak transcription	Right Atrium	heart
2	chr1:154516800-154521600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:154517000-154521600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:154517600-154523600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:154518000-154526000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:154518600-154521600	Weak transcription	NHLF	lung
7	chr1:154518600-154521800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:154518800-154521600	Weak transcription	Aorta	Aorta
9	chr1:154518800-154521600	Weak transcription	Hela-S3	cervix
10	chr1:154518800-154521800	Weak transcription	Fetal Brain Male	brain
11	chr1:154519000-154521600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:154519000-154521600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:154519000-154522600	Enhancers	Stomach Mucosa	stomach
14	chr1:154519400-154521600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:154519400-154521800	Weak transcription	K562	blood
16	chr1:154519600-154521600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:154519800-154521600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:154520000-154521600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:154520000-154521600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:154520000-154521600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:154520000-154521600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:154520000-154521800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:154520000-154521800	Genic enhancers	Fetal Intestine Large	intestine
24	chr1:154520000-154522000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:154520000-154522600	Weak transcription	Small Intestine	intestine
26	chr1:154520000-154528200	Strong transcription	Placenta	Placenta
27	chr1:154520200-154521600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr1:154520200-154521800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:154520200-154522000	Enhancers	Fetal Heart	heart
30	chr1:154520200-154522400	Weak transcription	Fetal Kidney	kidney
31	chr1:154520400-154521800	Weak transcription	Ovary	ovary
32	chr1:154520400-154522000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:154520400-154523400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:154520600-154521600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:154520600-154521800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:154520600-154522800	Genic enhancers	Brain Germinal Matrix	brain
37	chr1:154520600-154523200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:154520600-154528400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:154520600-154528800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:154520600-154528800	Strong transcription	Primary T cells from cord blood	blood
41	chr1:154520800-154521600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:154520800-154522200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:154520800-154528400	Strong transcription	Adipose Nuclei	Adipose
44	chr1:154520800-154528400	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr1:154520800-154528600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:154520800-154528800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:154521000-154522400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:154521000-154522400	Genic enhancers	Monocytes-CD14+_RO01746	blood
49	chr1:154521000-154528200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:154521000-154528200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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