Variant report

Variant	rs10010097
Chromosome Location	chr4:120440413-120440414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10003953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10012406	1.00[AMR][1000 genomes]
rs10015714	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015999	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017842	1.00[AMR][1000 genomes]
rs10021318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027735	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028634	1.00[AMR][1000 genomes]
rs10029882	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032392	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213498	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10471013	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11098519	1.00[AMR][1000 genomes]
rs11098520	1.00[AMR][1000 genomes]
rs28380652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28399227	1.00[AMR][1000 genomes]
rs28405434	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28419430	1.00[AMR][1000 genomes]
rs28436005	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450144	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28469881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470408	1.00[AMR][1000 genomes]
rs28535588	1.00[AMR][1000 genomes]
rs28576329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28590285	1.00[AMR][1000 genomes]
rs28615474	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28622207	1.00[AMR][1000 genomes]
rs28634062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639494	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639769	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28651206	1.00[AMR][1000 genomes]
rs28654414	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665114	1.00[AMR][1000 genomes]
rs28669906	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709577	1.00[AMR][1000 genomes]
rs28736368	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28864814	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28870820	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3872804	1.00[AMR][1000 genomes]
rs55905129	1.00[AMR][1000 genomes]
rs56191916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57295141	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57516186	1.00[AMR][1000 genomes]
rs59116083	1.00[AMR][1000 genomes]
rs61729464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61823285	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918555	1.00[AMR][1000 genomes]
rs72918590	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918597	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920619	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920685	1.00[AMR][1000 genomes]
rs9307478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884542	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9993996	1.00[AMR][1000 genomes]
rs9996803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997423	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998244	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 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	chr4:120377600-120441000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
4	chr4:120397800-120442600	Weak transcription	Hela-S3	cervix
5	chr4:120403400-120445800	Weak transcription	A549	lung
6	chr4:120417600-120445800	Weak transcription	NHEK	skin
7	chr4:120420200-120485400	Weak transcription	Fetal Brain Male	brain
8	chr4:120420400-120449600	Weak transcription	Brain Angular Gyrus	brain
9	chr4:120421000-120443600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:120421000-120445600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:120421200-120455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:120422000-120446400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:120422800-120446600	Weak transcription	Fetal Stomach	stomach
14	chr4:120422800-120448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:120423400-120450600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:120428000-120444800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr4:120430800-120447400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:120432400-120440600	Strong transcription	Primary B cells from cord blood	blood
19	chr4:120432400-120441200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:120432800-120443000	Strong transcription	Primary T cells from cord blood	blood
21	chr4:120433400-120441600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:120433400-120442600	Strong transcription	Fetal Thymus	thymus
23	chr4:120433400-120442800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:120433400-120442800	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:120433400-120444600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr4:120433600-120442200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:120433600-120442800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:120434600-120474400	Weak transcription	Gastric	stomach
29	chr4:120434800-120442600	Weak transcription	Psoas Muscle	Psoas
30	chr4:120434800-120444200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:120434800-120446000	Weak transcription	HSMMtube	muscle
32	chr4:120434800-120446200	Weak transcription	HMEC	breast
33	chr4:120434800-120446400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:120434800-120448200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:120434800-120455400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:120434800-120464800	Weak transcription	Lung	lung
37	chr4:120435000-120441800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr4:120435000-120457800	Weak transcription	Right Ventricle	heart
39	chr4:120435000-120473200	Weak transcription	Esophagus	oesophagus
40	chr4:120435000-120487600	Weak transcription	Colonic Mucosa	Colon
41	chr4:120435200-120442600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:120435200-120455800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:120435400-120442600	Weak transcription	Left Ventricle	heart
44	chr4:120435400-120448000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:120436000-120441600	Genic enhancers	NHLF	lung
46	chr4:120436200-120473800	Weak transcription	Fetal Brain Female	brain
47	chr4:120436600-120446000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:120436600-120452800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:120436600-120455000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:120436600-120456200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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