Variant report

Variant	rs41269097
Chromosome Location	chr1:45475886-45475887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45475794-45476076	MCF-7	breast:	n/a	n/a
2	MXI1	chr1:45475602-45477470	SK-N-SH	brain:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45469387..45472063-chr1:45473604..45475987,2	MCF-7	breast:
2	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
3	chr1:45193444..45198675-chr1:45475617..45480324,16	K562	blood:
4	chr1:45269727..45273120-chr1:45475175..45479286,6	K562	blood:
5	chr1:45474418..45476530-chr1:46048462..46051158,2	K562	blood:
6	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
7	chr1:45475180..45477058-chr1:45478388..45480349,2	MCF-7	breast:
8	chr1:45306981..45310503-chr1:45474976..45481200,7	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	chr1:45184334..45189289-chr1:45475449..45480431,12	K562	blood:

No data

Variant related genes	Relation type
HECTD3	TF binding region
UROD	TF binding region
ENSG00000202444	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000268949	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000117425	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]
rs41269101	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	chr1:45474600-45476000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
4	chr1:45474800-45476200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:45475000-45476000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:45475000-45476400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
7	chr1:45475200-45476000	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr1:45475200-45476000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:45475200-45476000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:45475200-45476000	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
11	chr1:45475200-45476000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
12	chr1:45475200-45476000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
13	chr1:45475200-45476000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
14	chr1:45475200-45476200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr1:45475200-45476400	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:45475200-45476600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:45475400-45476000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:45475400-45476000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:45475400-45476000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
20	chr1:45475400-45476000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
21	chr1:45475400-45476000	Flanking Active TSS	NHDF-Ad	bronchial
22	chr1:45475400-45476000	Transcr. at gene 5' and 3'	NHLF	lung
23	chr1:45475400-45476200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:45475400-45476200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:45475400-45476200	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr1:45475400-45476200	Flanking Active TSS	NH-A	brain
27	chr1:45475400-45476400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:45475400-45477600	Flanking Active TSS	Colonic Mucosa	Colon
29	chr1:45475600-45476000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:45475600-45476000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:45475600-45476000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:45475600-45476000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:45475600-45476000	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:45475600-45476000	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
35	chr1:45475600-45476000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
36	chr1:45475600-45476000	Flanking Active TSS	HMEC	breast
37	chr1:45475600-45476000	Flanking Active TSS	HSMM	muscle
38	chr1:45475600-45476200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:45475600-45476200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:45475600-45476200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:45475600-45476200	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr1:45475600-45476200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:45475600-45476200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:45475600-45476200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:45475600-45476200	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr1:45475600-45476200	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr1:45475600-45476200	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr1:45475600-45476200	Flanking Active TSS	Fetal Brain Male	brain
49	chr1:45475600-45476200	Flanking Active TSS	Left Ventricle	heart
50	chr1:45475600-45476200	Flanking Active TSS	Pancreas	Pancrea

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