Variant report

Variant	rs57295141
Chromosome Location	chr4:120403128-120403129
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120401525..120403278-chr4:120407490..120410209,2	MCF-7	breast:
2	chr4:120395792..120397416-chr4:120401451..120404061,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC110373.1-8	chr4:120402929-120403580	NONHSAT098084

Variant related genes	Relation type
ENSG00000245958	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10003953	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010097	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10012406	1.00[AMR][1000 genomes]
rs10015714	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015999	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017842	1.00[AMR][1000 genomes]
rs10021318	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023384	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027735	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028634	1.00[AMR][1000 genomes]
rs10029882	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031328	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032392	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213498	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10471013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11098519	1.00[AMR][1000 genomes]
rs11098520	1.00[AMR][1000 genomes]
rs28380652	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28399227	1.00[AMR][1000 genomes]
rs28405434	1.00[AMR][1000 genomes]
rs28419430	1.00[AMR][1000 genomes]
rs28436005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450144	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28469881	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470408	1.00[AMR][1000 genomes]
rs28535588	1.00[AMR][1000 genomes]
rs28576329	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28590285	1.00[AMR][1000 genomes]
rs28615474	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28622207	1.00[AMR][1000 genomes]
rs28634062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639494	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28651206	1.00[AMR][1000 genomes]
rs28654414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665114	1.00[AMR][1000 genomes]
rs28669906	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709577	1.00[AMR][1000 genomes]
rs28736368	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28864814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28870820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3872804	1.00[AMR][1000 genomes]
rs55905129	1.00[AMR][1000 genomes]
rs56191916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57516186	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59116083	1.00[AMR][1000 genomes]
rs61729464	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61823285	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918555	1.00[AMR][1000 genomes]
rs72918590	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920685	1.00[AMR][1000 genomes]
rs9307478	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884290	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884542	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9993996	1.00[AMR][1000 genomes]
rs9996803	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997423	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998244	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv879847	chr4:120371729-120450159	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv964092	chr4:120392750-120412350	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	esv1802153	chr4:120397829-120457682	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120376400-120471600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:120376600-120419200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:120377000-120416000	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:120377200-120403400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:120377200-120415600	Weak transcription	Brain Substantia Nigra	brain
6	chr4:120377200-120416200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:120377200-120419600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:120377200-120433800	Weak transcription	Gastric	stomach
9	chr4:120377400-120415200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:120377400-120416200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:120377400-120439000	Weak transcription	Small Intestine	intestine
12	chr4:120377400-120439000	Weak transcription	Spleen	Spleen
13	chr4:120377600-120441000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
15	chr4:120384400-120439200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:120384600-120416200	Weak transcription	Fetal Brain Male	brain
17	chr4:120387400-120403600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:120390400-120409400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:120390600-120409200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:120390800-120419800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:120391600-120408800	Weak transcription	NHDF-Ad	bronchial
22	chr4:120391600-120415600	Weak transcription	HUVEC	blood vessel
23	chr4:120393200-120419800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:120393800-120409800	Weak transcription	NH-A	brain
25	chr4:120394800-120415200	Weak transcription	NHEK	skin
26	chr4:120395600-120404800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:120396000-120404000	Strong transcription	Dnd41	blood
28	chr4:120397000-120403400	Strong transcription	Placenta	Placenta
29	chr4:120397200-120403600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:120397600-120415000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:120397800-120403200	Weak transcription	Fetal Lung	lung
32	chr4:120397800-120404800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:120397800-120416400	Weak transcription	HSMMtube	muscle
34	chr4:120397800-120442600	Weak transcription	Hela-S3	cervix
35	chr4:120398200-120419600	Weak transcription	Fetal Stomach	stomach
36	chr4:120398400-120403800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:120398600-120403600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:120398800-120420000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:120399200-120431200	Weak transcription	Fetal Heart	heart
40	chr4:120399600-120403200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:120399600-120403800	Strong transcription	Primary B cells from cord blood	blood
42	chr4:120399600-120404400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:120400000-120404200	Strong transcription	Osteobl	bone
44	chr4:120400000-120404800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:120400200-120403800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:120400200-120404600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:120400400-120403400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:120400400-120403400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:120400400-120404200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:120400600-120403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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