Variant report

Variant	rs30619
Chromosome Location	chr5:14277686-14277687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14268455..14270737-chr5:14277018..14279367,2	MCF-7	breast:
2	chr5:14107611..14110388-chr5:14277452..14281941,4	MCF-7	breast:
3	chr5:14267248..14270111-chr5:14276512..14278649,2	K562	blood:
4	chr5:14143194..14145059-chr5:14276873..14279594,2	MCF-7	breast:
5	chr5:13987882..13988549-chr5:14277210..14277954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11747048	1.00[CHB][hapmap]
rs13175673	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13184211	1.00[CHB][hapmap]
rs13184670	1.00[CHB][hapmap]
rs164861	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299045	1.00[CHB][hapmap]
rs17302408	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs187125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434605	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs245577	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591277	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26057	1.00[CHB][hapmap]
rs26058	1.00[CHB][hapmap]
rs26059	1.00[CHB][hapmap]
rs26061	1.00[CHB][hapmap]
rs2607077	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607078	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697663	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27665	1.00[CHB][hapmap]
rs28010	1.00[CHB][hapmap]
rs30616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs30617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];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]
rs354285	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs354298	1.00[CHB][hapmap]
rs354300	1.00[CHB][hapmap]
rs354305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354308	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354312	1.00[CHB][hapmap]
rs3849082	1.00[CHB][hapmap]
rs39856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42485	1.00[ASN][1000 genomes]
rs4702028	1.00[CHB][hapmap]
rs706271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773703	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs773763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799025	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897724	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897726	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923616	1.00[CHB][hapmap];1.00[CHD][hapmap]

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	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
2	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
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs30619	TOX	trans	lymphoblastoid	seeQTL
rs30619	CHMP7	trans	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14265200-14293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:14265400-14284600	Weak transcription	Stomach Mucosa	stomach
3	chr5:14265400-14286600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:14268600-14291000	Weak transcription	Fetal Kidney	kidney
5	chr5:14269200-14280000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:14269200-14286400	Weak transcription	Pancreas	Pancrea
7	chr5:14269200-14286600	Weak transcription	Spleen	Spleen
8	chr5:14270200-14290800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:14270400-14278200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:14270400-14279800	Weak transcription	Ovary	ovary
11	chr5:14270400-14280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:14270400-14280400	Weak transcription	Placenta	Placenta
13	chr5:14270400-14280400	Weak transcription	Fetal Thymus	thymus
14	chr5:14270400-14280600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:14270400-14280600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:14270400-14280600	Weak transcription	Lung	lung
17	chr5:14270400-14283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:14270400-14284400	Weak transcription	Colonic Mucosa	Colon
19	chr5:14270400-14284600	Weak transcription	Brain Germinal Matrix	brain
20	chr5:14270400-14284800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:14270400-14284800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:14270400-14286400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:14270400-14286800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:14270400-14288800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:14270400-14289400	Weak transcription	Gastric	stomach
26	chr5:14270400-14293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:14270400-14305200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:14270400-14313600	Weak transcription	Small Intestine	intestine
29	chr5:14270600-14279800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:14270800-14279800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr5:14270800-14280200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:14270800-14280200	Weak transcription	Fetal Lung	lung
33	chr5:14270800-14280200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:14270800-14280400	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:14270800-14280600	Weak transcription	Fetal Intestine Large	intestine
36	chr5:14270800-14281400	Weak transcription	Fetal Stomach	stomach
37	chr5:14270800-14282000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:14270800-14286800	Weak transcription	Fetal Brain Male	brain
39	chr5:14270800-14293000	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:14271000-14280400	Weak transcription	Adipose Nuclei	Adipose
41	chr5:14271000-14295800	Weak transcription	Brain Angular Gyrus	brain
42	chr5:14271800-14280200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:14271800-14280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:14271800-14284400	Weak transcription	Aorta	Aorta
45	chr5:14272200-14280400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr5:14272200-14281600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:14272400-14279600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:14272400-14279600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr5:14272400-14280200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:14272400-14280400	Weak transcription	Liver	Liver

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