Variant report

Variant	rs9429499
Chromosome Location	chr1:113424837-113424838
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113422315..113424969-chr1:113580165..113583110,2	K562	blood:
2	chr1:113421698..113424854-chr1:113496536..113501677,6	K562	blood:
3	chr1:113424350..113426244-chr1:113426854..113428692,2	MCF-7	breast:
4	chr1:113392230..113394904-chr1:113422287..113425247,2	MCF-7	breast:
5	chr1:113423539..113425457-chr1:113613953..113617483,4	K562	blood:
6	chr1:113423643..113425440-chr1:113613953..113616307,2	K562	blood:
7	chr1:113424770..113426373-chr1:113429791..113432690,2	MCF-7	breast:
8	chr1:113424435..113426998-chr1:113430244..113432680,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000155380	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000224167	Chromatin interaction
ENSG00000238198	Chromatin interaction
ENSG00000198799	Chromatin interaction
ENSG00000215866	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10158316	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059435	1.00[EUR][1000 genomes]
rs12067118	1.00[EUR][1000 genomes]
rs12070103	1.00[EUR][1000 genomes]
rs12070165	1.00[EUR][1000 genomes]
rs17030801	1.00[EUR][1000 genomes]
rs17030825	1.00[EUR][1000 genomes]
rs17030972	1.00[EUR][1000 genomes]
rs3866218	1.00[EUR][1000 genomes]
rs3892517	1.00[EUR][1000 genomes]
rs41510545	1.00[EUR][1000 genomes]
rs55879014	1.00[EUR][1000 genomes]
rs57514267	1.00[EUR][1000 genomes]
rs57546902	1.00[EUR][1000 genomes]
rs58175041	1.00[EUR][1000 genomes]
rs60031820	1.00[EUR][1000 genomes]
rs60103137	1.00[EUR][1000 genomes]
rs60860858	1.00[EUR][1000 genomes]
rs61134101	1.00[EUR][1000 genomes]
rs6657154	1.00[EUR][1000 genomes]
rs6678201	1.00[EUR][1000 genomes]
rs6694556	1.00[EUR][1000 genomes]
rs6697225	1.00[EUR][1000 genomes]
rs72982471	1.00[EUR][1000 genomes]
rs72984355	1.00[EUR][1000 genomes]
rs72986328	1.00[EUR][1000 genomes]
rs72986329	1.00[EUR][1000 genomes]
rs72986335	1.00[EUR][1000 genomes]
rs72986336	1.00[EUR][1000 genomes]
rs72986345	1.00[EUR][1000 genomes]
rs73000304	1.00[EUR][1000 genomes]
rs73000323	1.00[EUR][1000 genomes]
rs73000328	1.00[EUR][1000 genomes]
rs7531239	1.00[EUR][1000 genomes]
rs7534668	1.00[EUR][1000 genomes]
rs7539797	1.00[EUR][1000 genomes]
rs7541153	1.00[EUR][1000 genomes]
rs9308259	1.00[EUR][1000 genomes]
rs9429498	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9429502	1.00[EUR][1000 genomes]
rs9429699	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9429703	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1008434	chr1:113288282-113447426	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
13	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
14	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
15	esv3362439	chr1:113376621-113450321	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113421400-113435200	Weak transcription	Fetal Heart	heart
2	chr1:113422000-113425800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr1:113423400-113425200	Enhancers	Brain Substantia Nigra	brain
4	chr1:113423400-113425400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:113423400-113425400	Enhancers	Brain Hippocampus Middle	brain
6	chr1:113423400-113425600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:113423400-113425600	Enhancers	NHEK	skin
8	chr1:113423400-113425800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:113423600-113425200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:113423600-113425400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:113423600-113425400	Enhancers	HMEC	breast
12	chr1:113423600-113425400	Enhancers	K562	blood
13	chr1:113423600-113425600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:113423600-113425600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:113423600-113425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:113423600-113425800	Enhancers	HSMM	muscle
17	chr1:113423600-113426000	Enhancers	Fetal Muscle Leg	muscle
18	chr1:113423600-113426200	Enhancers	Placenta	Placenta
19	chr1:113423800-113425200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:113423800-113425600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:113423800-113425800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:113423800-113425800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:113423800-113425800	Enhancers	Adipose Nuclei	Adipose
24	chr1:113423800-113425800	Enhancers	Duodenum Mucosa	Duodenum
25	chr1:113423800-113426600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:113424000-113425600	Enhancers	Colonic Mucosa	Colon
27	chr1:113424200-113425600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:113424200-113425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:113424200-113425800	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr1:113424400-113425000	Enhancers	Brain Anterior Caudate	brain
31	chr1:113424400-113425000	Enhancers	Fetal Intestine Large	intestine
32	chr1:113424400-113425200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:113424400-113425200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:113424400-113425200	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:113424400-113425600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:113424400-113425600	Enhancers	Fetal Intestine Small	intestine
37	chr1:113424400-113425800	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:113424400-113425800	Enhancers	Fetal Stomach	stomach
39	chr1:113424400-113425800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:113424400-113425800	Enhancers	HSMMtube	muscle
41	chr1:113424400-113426000	Flanking Active TSS	HepG2	liver
42	chr1:113424600-113425000	Enhancers	Colon Smooth Muscle	Colon
43	chr1:113424600-113425000	Flanking Active TSS	Stomach Mucosa	stomach
44	chr1:113424600-113425000	Flanking Active TSS	Osteobl	bone
45	chr1:113424600-113425400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:113424600-113425400	Enhancers	Placenta Amnion	Placenta Amnion
47	chr1:113424600-113425600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:113424600-113425600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:113424600-113425600	Enhancers	Esophagus	oesophagus
50	chr1:113424600-113425600	Enhancers	Right Atrium	heart

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