Variant report

Variant	rs1372243
Chromosome Location	chr4:102265785-102265786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102265718..102267485-chr4:103187307..103189886,2	MCF-7	breast:
2	chr4:102263328..102265199-chr4:102265515..102267436,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EMCN-3	chr4:102265025-102267178	NONHSAT097571

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1011849	0.97[AFR][1000 genomes]
rs1372244	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1441431	0.92[AFR][1000 genomes]
rs1561722	0.92[AFR][1000 genomes]
rs17031168	0.97[AFR][1000 genomes]
rs17031172	0.92[AFR][1000 genomes]
rs17031175	0.92[AFR][1000 genomes]
rs17031176	0.92[AFR][1000 genomes]
rs17031180	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031182	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3974659	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4488940	0.92[AFR][1000 genomes]
rs4504259	0.92[AFR][1000 genomes]
rs4637408	0.97[AFR][1000 genomes]
rs55667372	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58629361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59079781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59224049	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59763039	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60438397	0.91[AFR][1000 genomes]
rs60984918	0.92[AFR][1000 genomes]
rs6532924	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6532925	0.92[AFR][1000 genomes]
rs6532926	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6810812	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812094	0.92[AFR][1000 genomes]
rs6827528	0.92[AFR][1000 genomes]
rs6828025	0.92[AFR][1000 genomes]
rs6830390	0.92[AFR][1000 genomes]
rs6831471	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6832020	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6834721	0.97[AFR][1000 genomes]
rs6837858	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6842191	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6844844	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6846554	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6852282	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835923	0.93[AFR][1000 genomes]
rs73835924	0.97[AFR][1000 genomes]
rs73835931	0.97[AFR][1000 genomes]
rs73835933	0.97[AFR][1000 genomes]
rs73835934	0.92[AFR][1000 genomes]
rs73835935	0.92[AFR][1000 genomes]
rs73835936	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835937	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835938	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835939	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835940	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835941	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835943	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835944	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7661895	0.92[AFR][1000 genomes]
rs7664396	0.92[AFR][1000 genomes]
rs7671524	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102249600-102266400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:102250400-102265800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr4:102250600-102266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:102251200-102265800	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:102252000-102265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:102252200-102266000	Weak transcription	Fetal Lung	lung
7	chr4:102252800-102266400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:102254000-102266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:102255200-102266400	Weak transcription	Gastric	stomach
10	chr4:102255400-102266600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:102256400-102265800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr4:102256600-102266000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:102256800-102265800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:102256800-102266200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:102257000-102266400	Weak transcription	Left Ventricle	heart
16	chr4:102257000-102266400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:102257000-102266400	Weak transcription	Right Ventricle	heart
18	chr4:102257000-102266400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:102257600-102266600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:102258000-102266200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:102258200-102266400	Weak transcription	Spleen	Spleen
22	chr4:102258400-102266000	Weak transcription	HepG2	liver
23	chr4:102258800-102265800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:102258800-102265800	Weak transcription	Adipose Nuclei	Adipose
25	chr4:102258800-102266400	Weak transcription	HSMM	muscle
26	chr4:102259000-102265800	Weak transcription	Brain Germinal Matrix	brain
27	chr4:102259000-102266400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:102259200-102266600	Weak transcription	Pancreas	Pancrea
29	chr4:102259400-102265800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:102259400-102266200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:102259600-102265800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:102259600-102266000	Weak transcription	Osteobl	bone
33	chr4:102259800-102265800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:102260000-102265800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:102260400-102265800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:102260400-102265800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:102260400-102266000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:102260400-102266200	Weak transcription	Right Atrium	heart
39	chr4:102260400-102266400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:102260400-102266400	Weak transcription	Small Intestine	intestine
41	chr4:102260800-102265800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:102261800-102266600	Weak transcription	Placenta	Placenta
43	chr4:102262000-102266000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:102262600-102265800	Enhancers	A549	lung
45	chr4:102262600-102265800	Active TSS	GM12878-XiMat	blood
46	chr4:102262800-102265800	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:102262800-102266000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:102262800-102266200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:102263000-102265800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:102263400-102266400	Enhancers	Brain Substantia Nigra	brain

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