Variant report

Variant	rs2306057
Chromosome Location	chr4:73931170-73931171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:73918831..73921818-chr4:73928688..73931173,2	K562	blood:
2	chr4:73908713..73911964-chr4:73931003..73934099,3	K562	blood:
3	chr4:73929667..73932602-chr4:74087330..74089868,2	K562	blood:
4	chr4:73929823..73938112-chr4:74120693..74129342,27	K562	blood:
5	chr4:73918067..73922976-chr4:73929464..73933812,4	K562	blood:

Variant related genes	Relation type
ENSG00000132466	Chromatin interaction
ENSG00000272859	Chromatin interaction
ENSG00000250220	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10011483	0.83[YRI][hapmap]
rs10019296	0.83[YRI][hapmap]
rs10028486	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11933644	0.89[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs16849102	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16849106	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16849108	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16849146	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849150	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849151	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs16849185	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2061574	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061575	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061576	0.94[ASN][1000 genomes]
rs2061577	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2366716	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28373296	0.81[ASN][1000 genomes]
rs28460851	0.81[ASN][1000 genomes]
rs28709646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28776801	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs3796680	0.84[ASN][1000 genomes]
rs4019514	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4615148	0.86[ASN][1000 genomes]
rs4631009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4694589	0.90[ASN][1000 genomes]
rs56235322	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56382488	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57330350	0.97[ASN][1000 genomes]
rs61149200	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61468561	0.94[ASN][1000 genomes]
rs61661011	0.83[ASN][1000 genomes]
rs6824334	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6845845	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848243	1.00[CEU][hapmap]
rs6849701	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6851670	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72859248	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72859249	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7664144	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs7670286	0.94[ASN][1000 genomes]
rs7674847	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7675007	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7675027	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7676278	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7679277	0.89[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7687433	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7690799	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7691344	0.94[ASN][1000 genomes]
rs7692425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7692749	0.94[ASN][1000 genomes]
rs7694505	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][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	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv917017	chr4:73754127-74044830	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	esv1849323	chr4:73926670-74115116	Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2306057	C4orf7	cis	cerebellum	SCAN
rs2306057	ANKRD56	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73917200-73933800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:73917400-73932000	Weak transcription	Psoas Muscle	Psoas
3	chr4:73918600-73933000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:73918800-73932200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:73918800-73933400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:73919000-73931400	Strong transcription	Liver	Liver
7	chr4:73919000-73932000	Strong transcription	Fetal Thymus	thymus
8	chr4:73919000-73932600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:73919000-73932800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:73919200-73931200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr4:73919200-73931200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:73919200-73932200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:73919600-73931600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr4:73920200-73931400	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:73920600-73932400	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:73920800-73931400	Strong transcription	Dnd41	blood
17	chr4:73920800-73931800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:73920800-73934400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:73921000-73931200	Strong transcription	Adipose Nuclei	Adipose
20	chr4:73921000-73931600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr4:73921000-73933200	Strong transcription	Fetal Muscle Leg	muscle
22	chr4:73921000-73933600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:73921200-73933200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:73921400-73931800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:73921400-73934200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:73921600-73933800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:73921800-73933000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:73921800-73933200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:73922000-73933200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:73922200-73933600	Weak transcription	Hela-S3	cervix
31	chr4:73922400-73931400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:73922400-73931400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:73922600-73933000	Strong transcription	Fetal Stomach	stomach
34	chr4:73923200-73931400	Strong transcription	Primary T cells from cord blood	blood
35	chr4:73923200-73932800	Weak transcription	Small Intestine	intestine
36	chr4:73924000-73932000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:73924200-73933800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:73925200-73933800	Weak transcription	A549	lung
39	chr4:73925400-73933800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:73925400-73933800	Weak transcription	Aorta	Aorta
41	chr4:73925600-73932000	Weak transcription	Brain Angular Gyrus	brain
42	chr4:73925800-73933800	Weak transcription	Stomach Mucosa	stomach
43	chr4:73925800-73934000	Weak transcription	Ovary	ovary
44	chr4:73925800-73934000	Weak transcription	Right Ventricle	heart
45	chr4:73925800-73934400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:73925800-73934800	Weak transcription	Gastric	stomach
47	chr4:73926000-73933000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:73926000-73933600	Weak transcription	Fetal Brain Male	brain
49	chr4:73926000-73933800	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:73926000-73933800	Weak transcription	Colonic Mucosa	Colon

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