Variant report

Variant	rs2354942
Chromosome Location	chr4:48840545-48840546
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	chr4:48837731..48840257-chr4:48840429..48842446,2	K562	blood:
2	chr4:48835128..48837334-chr4:48839249..48842163,4	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10034207	0.82[YRI][hapmap]
rs10049760	0.82[YRI][hapmap]
rs10938545	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs11729557	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12507475	0.85[YRI][hapmap]
rs1533511	0.82[YRI][hapmap]
rs1712762	0.82[YRI][hapmap]
rs2138866	0.82[YRI][hapmap]
rs2354939	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2465262	0.97[AFR][1000 genomes]
rs2572340	0.97[AFR][1000 genomes]
rs2572341	0.83[AFR][1000 genomes]
rs2572342	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2572347	0.87[AFR][1000 genomes]
rs2605253	0.82[AFR][1000 genomes]
rs2712155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2925213	0.85[AFR][1000 genomes]
rs4274819	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4694905	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695406	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6815932	0.97[AFR][1000 genomes]
rs6824209	0.97[AFR][1000 genomes]
rs6839713	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844579	0.97[AFR][1000 genomes]
rs7654729	0.97[AFR][1000 genomes]
rs7667431	1.00[AMR][1000 genomes]
rs7669831	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7686458	0.84[AFR][1000 genomes]
rs7698064	0.82[YRI][hapmap]
rs7698768	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776581	0.82[YRI][hapmap]
rs9994214	0.82[YRI][hapmap]
rs9998178	0.82[YRI][hapmap]

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	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48834000-48859800	Weak transcription	Aorta	Aorta
2	chr4:48834000-48864600	Weak transcription	Stomach Mucosa	stomach
3	chr4:48834200-48847600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:48834800-48856600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:48835000-48846000	Weak transcription	Right Atrium	heart
6	chr4:48835000-48848600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:48835000-48858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:48835000-48859800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:48835000-48861400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:48835000-48862400	Strong transcription	Fetal Thymus	thymus
11	chr4:48835000-48863000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:48835000-48864400	Strong transcription	HSMM	muscle
13	chr4:48835200-48841200	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr4:48835200-48848600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:48835200-48863200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:48835200-48863800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:48835200-48864200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:48835400-48841000	Strong transcription	NHDF-Ad	bronchial
19	chr4:48835400-48842800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:48835400-48843800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:48835400-48844800	Weak transcription	Fetal Brain Male	brain
22	chr4:48835400-48850400	Strong transcription	K562	blood
23	chr4:48835400-48857400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:48835400-48863200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:48835400-48863400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:48835600-48841600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:48835600-48845400	Strong transcription	Osteobl	bone
28	chr4:48835600-48847400	Weak transcription	Fetal Heart	heart
29	chr4:48835600-48848600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:48835600-48856200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:48835600-48864000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:48835800-48843000	Strong transcription	Fetal Intestine Large	intestine
33	chr4:48835800-48845800	Strong transcription	Fetal Lung	lung
34	chr4:48835800-48848200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:48835800-48848400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr4:48835800-48856200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:48835800-48857000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:48835800-48857000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:48835800-48863200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:48836000-48842400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:48836000-48842400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr4:48836000-48844600	Weak transcription	Hela-S3	cervix
43	chr4:48836000-48849600	Strong transcription	Placenta	Placenta
44	chr4:48836000-48858000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:48836000-48863600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:48836200-48841400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:48836200-48842200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:48836200-48848800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:48836200-48854800	Strong transcription	Primary B cells from cord blood	blood
50	chr4:48836200-48863600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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