Variant report

Variant	rs10399919
Chromosome Location	chr1:113166489-113166490
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113160312..113164959-chr1:113166253..113170624,10	MCF-7	breast:
2	chr1:113155240..113157847-chr1:113166042..113168609,2	K562	blood:
3	chr1:112912405..112914289-chr1:113164040..113166594,2	K562	blood:
4	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
5	chr1:113077945..113080209-chr1:113165397..113168069,2	K562	blood:

Variant related genes	Relation type
ENSG00000238761	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000007341	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11102490	0.90[AFR][1000 genomes]
rs11102500	0.90[AFR][1000 genomes]
rs11102519	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102521	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060267	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069022	0.85[AFR][1000 genomes]
rs12069740	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080006	0.90[AFR][1000 genomes]
rs12082350	0.83[AFR][1000 genomes]
rs12087862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091635	0.90[AFR][1000 genomes]
rs12094504	0.85[AFR][1000 genomes]
rs12095563	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030446	0.83[AFR][1000 genomes]
rs17030451	0.83[AFR][1000 genomes]
rs17030455	0.85[AFR][1000 genomes]
rs17030475	0.90[AFR][1000 genomes]
rs17030592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4424506	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57573777	1.00[AMR][1000 genomes]
rs58634778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59053530	1.00[AMR][1000 genomes]
rs59324334	0.85[AFR][1000 genomes]
rs61203550	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982599	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984509	1.00[AMR][1000 genomes]
rs72984515	1.00[AMR][1000 genomes]
rs72986505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72986535	1.00[AMR][1000 genomes]
rs72993072	0.90[AFR][1000 genomes]
rs9919308	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163200-113167400	Weak transcription	Small Intestine	intestine
2	chr1:113163200-113167600	Weak transcription	Gastric	stomach
3	chr1:113163200-113168400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:113163200-113168400	Weak transcription	Pancreas	Pancrea
5	chr1:113163400-113168400	Weak transcription	Esophagus	oesophagus
6	chr1:113163400-113170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:113163600-113167600	Weak transcription	Ovary	ovary
8	chr1:113163600-113167600	Weak transcription	Right Ventricle	heart
9	chr1:113163600-113167800	Weak transcription	Aorta	Aorta
10	chr1:113163600-113167800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:113163600-113168000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:113163600-113171600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:113163600-113173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:113163600-113180600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
16	chr1:113163800-113167200	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:113163800-113167400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:113163800-113167400	Weak transcription	Fetal Heart	heart
19	chr1:113163800-113167600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:113163800-113167600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:113163800-113167600	Weak transcription	Right Atrium	heart
22	chr1:113163800-113167600	Weak transcription	Stomach Mucosa	stomach
23	chr1:113163800-113168200	Weak transcription	Fetal Lung	lung
24	chr1:113163800-113168200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:113163800-113168400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:113163800-113169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:113163800-113173200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:113163800-113176000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:113164000-113167600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:113164000-113167600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:113164000-113173200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:113164000-113190000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:113164200-113167600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:113164200-113167800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:113164200-113167800	Weak transcription	Fetal Stomach	stomach
38	chr1:113164200-113167800	Weak transcription	Left Ventricle	heart
39	chr1:113164200-113168200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:113164200-113168200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:113164200-113175800	Weak transcription	Fetal Brain Female	brain
42	chr1:113164200-113180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
44	chr1:113164400-113167400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:113164400-113167600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:113164400-113168400	Weak transcription	Fetal Intestine Large	intestine
47	chr1:113164600-113167800	Weak transcription	Spleen	Spleen
48	chr1:113164600-113168400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:113164600-113168400	Weak transcription	Lung	lung
50	chr1:113164600-113168400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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