Variant report

Variant	rs3846354
Chromosome Location	chr4:16251892-16251893
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:16227948..16229921-chr4:16249842..16252118,2	MCF-7	breast:
2	chr4:16182193..16183806-chr4:16249768..16252550,2	K562	blood:
3	chr4:16235269..16243012-chr4:16245014..16252154,9	K562	blood:

Variant related genes	Relation type
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11728731	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11735246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17559158	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2041541	0.81[EUR][1000 genomes]
rs2312941	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3846353	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41459449	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55863436	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6449220	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73118055	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7668272	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7677927	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7681211	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7695512	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7696623	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7698003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
4	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16229600-16254000	Weak transcription	Ovary	ovary
2	chr4:16229600-16254800	Weak transcription	Psoas Muscle	Psoas
3	chr4:16229800-16259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:16234000-16252000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:16234000-16252400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:16234000-16255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:16234200-16254400	Weak transcription	NHDF-Ad	bronchial
8	chr4:16234200-16257400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:16234200-16264800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:16234400-16252200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:16234400-16261600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:16234800-16253800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:16235000-16252200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:16235400-16272800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:16235600-16261600	Weak transcription	Fetal Kidney	kidney
16	chr4:16236200-16252400	Weak transcription	Right Ventricle	heart
17	chr4:16236200-16257400	Weak transcription	Left Ventricle	heart
18	chr4:16237200-16257400	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:16237600-16254800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:16238200-16258800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:16238200-16266000	Weak transcription	Fetal Brain Male	brain
22	chr4:16238400-16258400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:16240000-16259800	Weak transcription	Fetal Lung	lung
24	chr4:16240400-16263400	Weak transcription	Fetal Thymus	thymus
25	chr4:16242000-16254200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:16242200-16257600	Weak transcription	Gastric	stomach
27	chr4:16242200-16267800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:16243000-16258000	Weak transcription	Esophagus	oesophagus
29	chr4:16243400-16255200	Weak transcription	Small Intestine	intestine
30	chr4:16243400-16259200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:16243600-16252400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:16244000-16265000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr4:16244200-16258200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:16244400-16254000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:16244800-16253800	Weak transcription	Placenta	Placenta
36	chr4:16245000-16252400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:16245000-16252400	Weak transcription	Pancreas	Pancrea
38	chr4:16245000-16252400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:16245000-16261200	Weak transcription	Spleen	Spleen
40	chr4:16245600-16266000	Weak transcription	Brain Angular Gyrus	brain
41	chr4:16246000-16253600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:16246000-16255200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:16246000-16261400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:16246400-16258000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:16246400-16259200	Weak transcription	Thymus	Thymus
46	chr4:16246600-16257200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr4:16247400-16252000	Weak transcription	Osteobl	bone
48	chr4:16247800-16252000	Weak transcription	NHLF	lung
49	chr4:16248200-16252000	Weak transcription	Fetal Intestine Small	intestine
50	chr4:16248200-16252200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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