Variant report

Variant	rs10888406
Chromosome Location	chr1:151166896-151166897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151166739-151169180	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:151166741-151167272	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:151166814-151168106	HCT-116	colon:	n/a	n/a
4	POLR2A	chr1:151166415-151169060	Hela-S3	cervix:	n/a	n/a
5	RPC155	chr1:151166800-151167527	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:151166850-151167665	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151162057..151164706-chr1:151165181..151172008,8	K562	blood:
2	chr1:151166423..151168363-chr1:151318010..151319809,2	MCF-7	breast:
3	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
4	chr1:151156826..151164982-chr1:151165389..151172985,25	MCF-7	breast:
5	chr1:151166432..151169145-chr1:151169439..151172527,5	MCF-7	breast:
6	chr1:151166438..151169666-chr1:151298490..151301352,3	MCF-7	breast:
7	chr1:151166663..151167230-chr16:86542630..86543521,2	Hela-S3	cervix:
8	chr1:151164944..151168688-chr1:151252728..151255250,4	MCF-7	breast:
9	chr1:151041779..151043840-chr1:151166772..151169795,3	MCF-7	breast:

No data

Variant related genes	Relation type
PIP5K1A	TF binding region
VPS72	TF binding region
ENSG00000143398	Chromatin interaction
ENSG00000268388	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000163159	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10749660	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204785	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11807075	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12022732	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12062719	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12080778	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12407426	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16827941	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16833079	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892196	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4291501	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4520422	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970943	0.80[AMR][1000 genomes]
rs4970944	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971013	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971015	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971016	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971021	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971023	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971026	0.81[EUR][1000 genomes]
rs58323986	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817972	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587559	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6681071	0.81[EUR][1000 genomes]
rs6681163	0.81[EUR][1000 genomes]
rs6683396	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6686402	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6695344	0.87[ASN][1000 genomes]
rs6701325	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521064	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7527032	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7532935	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7539584	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7544947	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151162800-151167800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:151162800-151170200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:151162800-151170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:151163000-151170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:151163200-151167000	Weak transcription	Stomach Mucosa	stomach
6	chr1:151163200-151167600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:151163200-151167600	Weak transcription	HSMM	muscle
8	chr1:151163200-151167800	Weak transcription	Adipose Nuclei	Adipose
9	chr1:151163200-151168600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:151163200-151168600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:151163200-151170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:151163200-151170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:151163200-151170400	Weak transcription	Gastric	stomach
14	chr1:151163200-151170400	Weak transcription	Left Ventricle	heart
15	chr1:151163400-151167200	Weak transcription	HUVEC	blood vessel
16	chr1:151163400-151167600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:151163400-151167800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:151163400-151167800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:151163400-151167800	Weak transcription	Fetal Intestine Small	intestine
20	chr1:151163400-151167800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:151163400-151167800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:151163400-151167800	Weak transcription	NH-A	brain
23	chr1:151163400-151168200	Weak transcription	GM12878-XiMat	blood
24	chr1:151163400-151168600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:151163400-151168600	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:151163400-151168600	Weak transcription	Psoas Muscle	Psoas
27	chr1:151163400-151168800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:151163400-151168800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:151163400-151169000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:151163400-151170000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:151163400-151170200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:151163400-151170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:151163400-151170200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:151163400-151170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:151163400-151170200	Weak transcription	Brain Substantia Nigra	brain
36	chr1:151163400-151170400	Weak transcription	Primary T cells from cord blood	blood
37	chr1:151163600-151167200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:151163600-151167800	Weak transcription	Osteobl	bone
39	chr1:151163600-151168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:151163600-151170200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:151163600-151170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:151163600-151170200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:151163800-151167800	Weak transcription	HepG2	liver
44	chr1:151163800-151168600	Weak transcription	Dnd41	blood
45	chr1:151163800-151168800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:151163800-151169000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:151163800-151169000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:151166200-151167800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:151166400-151167000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr1:151166400-151167200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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