Variant report

Variant	rs62574346
Chromosome Location	chr9:96725350-96725351
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96581901..96582443-chr9:96724981..96725856,2	MCF-7	breast:
2	chr9:96656015..96657684-chr9:96723768..96726547,2	MCF-7	breast:
3	chr9:96671163..96671742-chr9:96725208..96725792,2	MCF-7	breast:
4	chr9:96582647..96583512-chr9:96725049..96725919,3	MCF-7	breast:
5	chr9:96712713..96719267-chr9:96721537..96727951,10	MCF-7	breast:
6	chr9:96674702..96676543-chr9:96724873..96726532,2	K562	blood:
7	chr9:95921974..95922852-chr9:96725322..96725880,3	K562	blood:
8	chr9:96444128..96445167-chr9:96724637..96725907,10	K562	blood:
9	chr9:96447198..96448012-chr9:96724180..96725782,4	MCF-7	breast:
10	chr9:96582631..96583817-chr9:96724571..96725838,5	MCF-7	breast:
11	chr9:96447168..96447681-chr9:96724934..96725916,2	K562	blood:
12	chr9:96724820..96727040-chr9:96730080..96732897,2	K562	blood:
13	chr9:96443153..96443849-chr9:96725175..96725852,2	K562	blood:
14	chr9:96622372..96623312-chr9:96724925..96725807,3	MCF-7	breast:
15	chr9:96576702..96577356-chr9:96724518..96725590,3	MCF-7	breast:
16	chr9:96672827..96673633-chr9:96725329..96725969,2	K562	blood:
17	chr9:96593842..96594413-chr9:96724983..96725802,2	MCF-7	breast:
18	chr9:96725158..96725897-chr9:96975460..96976466,4	K562	blood:
19	chr9:96444184..96445089-chr9:96724737..96725876,7	MCF-7	breast:
20	chr9:96671241..96673198-chr9:96724070..96726611,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235601	Chromatin interaction
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10821273	0.83[AFR][1000 genomes]
rs10993017	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11788160	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11788176	0.81[EUR][1000 genomes]
rs11789015	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11792744	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11793856	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12001386	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12004383	0.82[EUR][1000 genomes]
rs12684081	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1411861	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2095777	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2153791	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2398893	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34849895	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35001304	0.91[AFR][1000 genomes]
rs35480828	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35886839	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4316201	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4437716	0.82[AFR][1000 genomes]
rs5014099	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55947603	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56285369	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56335449	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62574323	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849645	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7858520	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96723000-96725800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr9:96723000-96728800	Weak transcription	Pancreas	Pancrea
3	chr9:96723000-96729800	Weak transcription	Gastric	stomach
4	chr9:96723200-96725400	Enhancers	Hela-S3	cervix
5	chr9:96724200-96725400	Enhancers	Stomach Mucosa	stomach
6	chr9:96724200-96725800	Enhancers	Fetal Stomach	stomach
7	chr9:96724600-96725600	Enhancers	Osteobl	bone
8	chr9:96724800-96725600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:96724800-96725800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr9:96724800-96725800	Enhancers	Colon Smooth Muscle	Colon
11	chr9:96724800-96726400	Enhancers	Placenta	Placenta
12	chr9:96725000-96725400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:96725000-96725400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:96725000-96725400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr9:96725000-96725400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
16	chr9:96725000-96725400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr9:96725000-96725400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:96725000-96725400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr9:96725000-96725400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:96725000-96725400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:96725000-96725400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:96725000-96725400	Enhancers	Brain Anterior Caudate	brain
23	chr9:96725000-96725400	Bivalent Enhancer	Fetal Intestine Small	intestine
24	chr9:96725000-96725400	Bivalent Enhancer	Fetal Thymus	thymus
25	chr9:96725000-96725400	Enhancers	Left Ventricle	heart
26	chr9:96725000-96725400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
27	chr9:96725000-96725400	Enhancers	Dnd41	blood
28	chr9:96725000-96725400	Enhancers	NHDF-Ad	bronchial
29	chr9:96725000-96725600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr9:96725000-96725600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr9:96725000-96725600	Enhancers	Adipose Nuclei	Adipose
32	chr9:96725000-96725600	Enhancers	HSMM	muscle
33	chr9:96725000-96725800	Enhancers	H9 Cell Line	embryonic stem cell
34	chr9:96725000-96725800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
35	chr9:96725000-96725800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
36	chr9:96725000-96725800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:96725000-96725800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr9:96725000-96725800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr9:96725000-96725800	Enhancers	Liver	Liver
40	chr9:96725000-96725800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
41	chr9:96725000-96725800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr9:96725000-96725800	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr9:96725000-96725800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr9:96725000-96725800	Enhancers	K562	blood
45	chr9:96725000-96726600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr9:96725000-96726800	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr9:96725000-96727400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:96725200-96725400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
49	chr9:96725200-96725400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
50	chr9:96725200-96725400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood

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