Variant report

Variant	rs73090954
Chromosome Location	chr1:227729641-227729642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227721537..227724263-chr1:227727527..227730135,2	MCF-7	breast:
2	chr1:227725139..227726773-chr1:227727190..227729662,2	K562	blood:
3	chr1:227725436..227728346-chr1:227728933..227731230,4	MCF-7	breast:
4	chr1:227728970..227731707-chr1:227751101..227754291,3	MCF-7	breast:
5	chr1:227726703..227728573-chr1:227729012..227731358,2	K562	blood:
6	chr1:227729010..227735281-chr1:227748522..227752811,6	MCF-7	breast:
7	chr1:227727960..227729815-chr1:228131832..228133962,2	MCF-7	breast:
8	chr1:227728158..227729940-chr1:227914897..227917653,2	MCF-7	breast:
9	chr1:227728577..227730296-chr1:227730401..227732480,2	MCF-7	breast:
10	chr1:227729455..227731523-chr1:227733555..227735249,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202264	Chromatin interaction
ENSG00000181450	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12563564	1.00[ASN][1000 genomes]
rs12564917	1.00[ASN][1000 genomes]
rs12565099	0.81[ASN][1000 genomes]
rs12565618	1.00[ASN][1000 genomes]
rs12565653	1.00[ASN][1000 genomes]
rs12567084	1.00[ASN][1000 genomes]
rs12567934	0.81[ASN][1000 genomes]
rs1323021	0.81[ASN][1000 genomes]
rs16841323	1.00[ASN][1000 genomes]
rs16847912	1.00[ASN][1000 genomes]
rs16847926	1.00[ASN][1000 genomes]
rs16847929	1.00[ASN][1000 genomes]
rs16847948	1.00[ASN][1000 genomes]
rs16847987	1.00[ASN][1000 genomes]
rs16848044	0.81[ASN][1000 genomes]
rs16859962	1.00[ASN][1000 genomes]
rs16860227	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17492440	1.00[ASN][1000 genomes]
rs17492447	1.00[ASN][1000 genomes]
rs2101862	1.00[ASN][1000 genomes]
rs2313220	1.00[ASN][1000 genomes]
rs34984248	0.94[ASN][1000 genomes]
rs35703429	0.94[ASN][1000 genomes]
rs4462138	0.81[ASN][1000 genomes]
rs58961542	0.94[ASN][1000 genomes]
rs59461077	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6665512	1.00[ASN][1000 genomes]
rs73090936	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73090937	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73090938	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73090948	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73090952	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73090985	1.00[ASN][1000 genomes]
rs73090986	1.00[ASN][1000 genomes]
rs73090987	1.00[ASN][1000 genomes]
rs73090994	1.00[ASN][1000 genomes]
rs73091000	1.00[ASN][1000 genomes]
rs73092607	1.00[ASN][1000 genomes]
rs73092610	1.00[ASN][1000 genomes]
rs7533013	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7546845	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7554851	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7554870	1.00[ASN][1000 genomes]
rs996226	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227728800-227730400	Active TSS	Brain Anterior Caudate	brain
2	chr1:227729000-227729800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr1:227729000-227729800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:227729200-227729800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:227729200-227729800	Enhancers	Fetal Lung	lung
6	chr1:227729200-227729800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr1:227729200-227730000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:227729200-227730000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr1:227729200-227730200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:227729200-227730400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:227729200-227730400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr1:227729200-227730400	Active TSS	Colon Smooth Muscle	Colon
13	chr1:227729200-227730400	Active TSS	Fetal Brain Female	brain
14	chr1:227729200-227730400	Active TSS	Rectal Smooth Muscle	rectum
15	chr1:227729200-227730600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:227729200-227731000	Active TSS	Colonic Mucosa	Colon
17	chr1:227729400-227729800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:227729400-227729800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:227729400-227729800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:227729400-227729800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:227729400-227729800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:227729400-227729800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:227729400-227729800	Flanking Active TSS	Liver	Liver
24	chr1:227729400-227729800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr1:227729400-227729800	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr1:227729400-227729800	Flanking Active TSS	Placenta	Placenta
27	chr1:227729400-227729800	Bivalent Enhancer	Fetal Thymus	thymus
28	chr1:227729400-227729800	Flanking Active TSS	Gastric	stomach
29	chr1:227729400-227729800	Flanking Active TSS	Pancreas	Pancrea
30	chr1:227729400-227729800	Flanking Active TSS	Right Ventricle	heart
31	chr1:227729400-227729800	Flanking Active TSS	HUVEC	blood vessel
32	chr1:227729400-227730000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr1:227729400-227730000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:227729400-227730000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:227729400-227730000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:227729400-227730000	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr1:227729400-227730000	Flanking Active TSS	NH-A	brain
38	chr1:227729400-227730200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:227729400-227730200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
40	chr1:227729400-227730200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:227729400-227730200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
42	chr1:227729400-227730400	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:227729400-227730400	Active TSS	Brain Cingulate Gyrus	brain
44	chr1:227729400-227730400	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr1:227729400-227730600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:227729400-227730600	Active TSS	Fetal Intestine Large	intestine
47	chr1:227729400-227730600	Active TSS	Fetal Stomach	stomach
48	chr1:227729400-227730600	Active TSS	Left Ventricle	heart
49	chr1:227729400-227730600	Active TSS	Osteobl	bone
50	chr1:227729400-227730800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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