Variant report

Variant	rs30616
Chromosome Location	chr5:14267173-14267174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:14155881..14158811-chr5:14267142..14271683,5	MCF-7	breast:
2	chr5:14036740..14039261-chr5:14266762..14269658,3	MCF-7	breast:
3	chr5:14152626..14154635-chr5:14265361..14268345,3	MCF-7	breast:
4	chr5:14266100..14268810-chr5:14315325..14317635,2	K562	blood:
5	chr5:14264035..14266359-chr5:14267149..14269027,3	MCF-7	breast:
6	chr5:14217255..14219345-chr5:14264896..14267843,2	MCF-7	breast:
7	chr5:14110016..14111938-chr5:14264952..14267387,2	MCF-7	breast:
8	chr5:14142083..14147002-chr5:14262644..14273159,29	MCF-7	breast:
9	chr5:14142928..14148372-chr5:14263664..14268038,8	MCF-7	breast:
10	chr5:14034068..14036123-chr5:14267082..14269872,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11747048	1.00[CHB][hapmap]
rs13175673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13184211	1.00[CHB][hapmap]
rs13184670	1.00[CHB][hapmap]
rs164861	1.00[ASN][1000 genomes]
rs17299045	1.00[CHB][hapmap]
rs17302408	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187125	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs2434605	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs245577	1.00[ASN][1000 genomes]
rs26057	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs26058	1.00[CHB][hapmap]
rs26059	1.00[CHB][hapmap]
rs26061	1.00[CHB][hapmap]
rs2607077	1.00[ASN][1000 genomes]
rs2607078	1.00[ASN][1000 genomes]
rs2697663	1.00[ASN][1000 genomes]
rs27665	1.00[CHB][hapmap]
rs28010	1.00[CHB][hapmap]
rs30617	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs30619	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs30620	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs32339	1.00[CHB][hapmap]
rs32341	1.00[CHB][hapmap]
rs32390	1.00[CHB][hapmap]
rs32394	1.00[CHB][hapmap]
rs34045422	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs354285	1.00[CHB][hapmap]
rs354298	1.00[CHB][hapmap]
rs354300	1.00[CHB][hapmap]
rs354305	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs354308	1.00[ASN][1000 genomes]
rs354312	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs3849082	1.00[CHB][hapmap]
rs39856	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs42485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702028	1.00[CHB][hapmap]
rs706271	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs71614082	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs773701	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs773702	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs773703	1.00[CHB][hapmap]
rs773763	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs799025	1.00[ASN][1000 genomes]
rs897724	1.00[ASN][1000 genomes]
rs897726	1.00[ASN][1000 genomes]
rs923616	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14259000-14268400	Weak transcription	Esophagus	oesophagus
2	chr5:14259200-14267400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:14259200-14268400	Weak transcription	Spleen	Spleen
4	chr5:14259200-14268600	Weak transcription	Gastric	stomach
5	chr5:14261600-14268200	Weak transcription	Small Intestine	intestine
6	chr5:14261800-14268600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:14262200-14270800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:14262400-14268400	Weak transcription	Right Ventricle	heart
9	chr5:14262600-14267400	Weak transcription	Lung	lung
10	chr5:14262600-14268600	Weak transcription	Pancreas	Pancrea
11	chr5:14265200-14267200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:14265200-14268200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:14265200-14268400	Weak transcription	Colonic Mucosa	Colon
14	chr5:14265200-14268400	Weak transcription	Fetal Intestine Large	intestine
15	chr5:14265200-14268600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:14265200-14268800	Enhancers	HSMMtube	muscle
17	chr5:14265200-14271400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:14265200-14293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:14265400-14267200	Enhancers	Brain Germinal Matrix	brain
20	chr5:14265400-14267400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:14265400-14267600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:14265400-14267600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:14265400-14267800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:14265400-14267800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr5:14265400-14268000	Weak transcription	Brain Angular Gyrus	brain
26	chr5:14265400-14268000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:14265400-14268200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr5:14265400-14268200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:14265400-14268200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:14265400-14268200	Weak transcription	Brain Substantia Nigra	brain
31	chr5:14265400-14268200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:14265400-14268200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:14265400-14268200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:14265400-14268200	Enhancers	NHDF-Ad	bronchial
35	chr5:14265400-14268200	Enhancers	Osteobl	bone
36	chr5:14265400-14268400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:14265400-14268400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:14265400-14268400	Weak transcription	Adipose Nuclei	Adipose
39	chr5:14265400-14268400	Enhancers	Fetal Heart	heart
40	chr5:14265400-14268400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:14265400-14268400	Weak transcription	Fetal Stomach	stomach
42	chr5:14265400-14268400	Enhancers	HMEC	breast
43	chr5:14265400-14268600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:14265400-14268600	Enhancers	NHEK	skin
45	chr5:14265400-14269000	Weak transcription	Liver	Liver
46	chr5:14265400-14269200	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr5:14265400-14269400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr5:14265400-14269400	Weak transcription	Fetal Intestine Small	intestine
49	chr5:14265400-14269400	Weak transcription	Fetal Lung	lung
50	chr5:14265400-14269600	Weak transcription	Duodenum Mucosa	Duodenum

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