Variant report

Variant	rs41269101
Chromosome Location	chr1:45476007-45476008
allele	A/G
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:19)
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	SIN3AK20	chr1:45475934-45478388	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:45475794-45476076	MCF-7	breast:	n/a	n/a
3	MXI1	chr1:45475602-45477470	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:45475934-45477219	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr1:45475976-45477123	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:45475966-45476042	HUVEC	blood vessel:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
2	chr1:45193444..45198675-chr1:45475617..45480324,16	K562	blood:
3	chr1:45269727..45273120-chr1:45475175..45479286,6	K562	blood:
4	chr1:45474418..45476530-chr1:46048462..46051158,2	K562	blood:
5	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
6	chr1:45475180..45477058-chr1:45478388..45480349,2	MCF-7	breast:
7	chr1:45306981..45310503-chr1:45474976..45481200,7	K562	blood:
8	chr1:45449901..45454181-chr1:45475970..45480540,16	K562	blood:
9	chr1:45268954..45275189-chr1:45475024..45480055,7	K562	blood:
10	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
11	chr1:45194719..45198675-chr1:45474706..45481379,10	K562	blood:
12	chr1:45184334..45189303-chr1:45475138..45480545,18	K562	blood:
13	chr1:45455788..45461421-chr1:45474837..45478788,5	MCF-7	breast:
14	chr1:45283389..45288095-chr1:45474959..45480313,6	MCF-7	breast:
15	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
16	chr1:45273315..45275597-chr1:45475668..45479411,4	K562	blood:
17	chr1:45475963..45478525-chr1:45804448..45806898,2	MCF-7	breast:
18	chr1:45184334..45189289-chr1:45475449..45480431,12	K562	blood:
19	chr1:45470053..45471669-chr1:45475976..45477628,2	MCF-7	breast:

No data

Variant related genes	Relation type
UROD	TF binding region
HECTD3	TF binding region
ENSG00000268949	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11573544	0.86[ASN][1000 genomes]
rs2234479	0.87[ASN][1000 genomes]
rs2355951	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263958	0.86[ASN][1000 genomes]
rs263993	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264000	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264016	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738249	0.86[ASN][1000 genomes]
rs41269097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41306605	0.87[ASN][1000 genomes]
rs449870	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660292	0.87[ASN][1000 genomes]
rs474207	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506691	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429554	0.87[ASN][1000 genomes]
rs7512137	0.87[ASN][1000 genomes]
rs7533668	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45467000-45476400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45474200-45476200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:45474800-45476200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:45475000-45476400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr1:45475200-45476200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr1:45475200-45476400	Flanking Active TSS	GM12878-XiMat	blood
7	chr1:45475200-45476600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:45475400-45476200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:45475400-45476200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:45475400-45476200	Flanking Active TSS	Rectal Smooth Muscle	rectum
11	chr1:45475400-45476200	Flanking Active TSS	NH-A	brain
12	chr1:45475400-45476400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:45475400-45477600	Flanking Active TSS	Colonic Mucosa	Colon
14	chr1:45475600-45476200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:45475600-45476200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:45475600-45476200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:45475600-45476200	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr1:45475600-45476200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:45475600-45476200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:45475600-45476200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:45475600-45476200	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr1:45475600-45476200	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr1:45475600-45476200	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr1:45475600-45476200	Flanking Active TSS	Fetal Brain Male	brain
25	chr1:45475600-45476200	Flanking Active TSS	Left Ventricle	heart
26	chr1:45475600-45476200	Flanking Active TSS	Pancreas	Pancrea
27	chr1:45475600-45476200	Flanking Active TSS	Psoas Muscle	Psoas
28	chr1:45475600-45476200	Flanking Active TSS	Hela-S3	cervix
29	chr1:45475600-45476200	Flanking Active TSS	HepG2	liver
30	chr1:45475600-45476200	Flanking Active TSS	HUVEC	blood vessel
31	chr1:45475600-45476200	Flanking Active TSS	Osteobl	bone
32	chr1:45475600-45476400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:45475600-45476400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:45475600-45476400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr1:45475600-45476400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr1:45475600-45476400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr1:45475600-45476400	Flanking Active TSS	Liver	Liver
38	chr1:45475600-45476400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:45475600-45476400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr1:45475600-45476400	Flanking Active TSS	Spleen	Spleen
41	chr1:45475600-45476600	Flanking Active TSS	Dnd41	blood
42	chr1:45475600-45476600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:45475600-45477000	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr1:45475600-45477000	Active TSS	HSMMtube	muscle
45	chr1:45475600-45477200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:45475600-45477200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:45475600-45477200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:45475600-45480400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:45475800-45476200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr1:45475800-45476200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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