Variant report

Variant	rs16822379
Chromosome Location	chr1:184027676-184027677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184027158..184029769-chr1:184121429..184123845,2	K562	blood:
2	chr1:184018296..184023402-chr1:184024617..184032965,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198860	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1034477	0.88[ASN][1000 genomes]
rs10797941	0.88[ASN][1000 genomes]
rs11576332	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582961	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11585756	0.88[ASN][1000 genomes]
rs12086203	0.83[ASN][1000 genomes]
rs12402790	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12403064	0.94[ASN][1000 genomes]
rs12408961	0.94[ASN][1000 genomes]
rs12411231	0.94[ASN][1000 genomes]
rs12725276	0.88[ASN][1000 genomes]
rs12729638	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12734950	1.00[ASN][1000 genomes]
rs12751711	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759837	0.94[ASN][1000 genomes]
rs1409812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926873	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991170	0.88[ASN][1000 genomes]
rs34010717	0.88[ASN][1000 genomes]
rs34876045	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35178058	0.88[ASN][1000 genomes]
rs35514700	0.88[ASN][1000 genomes]
rs35947721	0.88[ASN][1000 genomes]
rs4650654	0.88[ASN][1000 genomes]
rs56239295	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58322431	0.94[ASN][1000 genomes]
rs61477737	0.88[ASN][1000 genomes]
rs68130131	0.88[ASN][1000 genomes]
rs73053551	0.94[ASN][1000 genomes]
rs765224	0.93[ASW][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs765225	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv533206	chr1:183861204-184091272	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16822379	C1orf19	Cis_1M	lymphoblastoid	RTeQTL
rs16822379	TSEN15	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184021600-184028600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:184021600-184029400	Weak transcription	Spleen	Spleen
3	chr1:184021600-184030600	Weak transcription	Colonic Mucosa	Colon
4	chr1:184021600-184033200	Weak transcription	Pancreas	Pancrea
5	chr1:184021600-184050400	Weak transcription	Gastric	stomach
6	chr1:184021600-184055800	Weak transcription	Esophagus	oesophagus
7	chr1:184021800-184034600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:184021800-184042000	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:184022000-184028800	Weak transcription	Fetal Brain Female	brain
10	chr1:184022000-184035400	Weak transcription	Brain Germinal Matrix	brain
11	chr1:184022000-184037600	Weak transcription	Right Ventricle	heart
12	chr1:184022000-184042000	Weak transcription	Psoas Muscle	Psoas
13	chr1:184022000-184043600	Weak transcription	Fetal Brain Male	brain
14	chr1:184022200-184044000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:184022200-184048800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:184022200-184053200	Weak transcription	Fetal Intestine Small	intestine
17	chr1:184022800-184029400	Weak transcription	Fetal Kidney	kidney
18	chr1:184023000-184028600	Weak transcription	Adipose Nuclei	Adipose
19	chr1:184023000-184034600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:184023000-184037400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:184023000-184037600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:184023000-184037600	Weak transcription	Brain Substantia Nigra	brain
23	chr1:184023000-184041000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:184023000-184041400	Weak transcription	Liver	Liver
25	chr1:184023000-184044000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:184023000-184044200	Weak transcription	HMEC	breast
27	chr1:184023000-184045200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:184023200-184028200	Weak transcription	GM12878-XiMat	blood
29	chr1:184023200-184028600	Weak transcription	Fetal Intestine Large	intestine
30	chr1:184023400-184028800	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:184023400-184052000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:184023600-184044200	Weak transcription	Brain Anterior Caudate	brain
33	chr1:184023800-184029800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:184023800-184030400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:184024400-184028800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:184024400-184045600	Weak transcription	Small Intestine	intestine
37	chr1:184024600-184028200	Weak transcription	Primary B cells from cord blood	blood
38	chr1:184024600-184028600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:184024600-184028600	Weak transcription	Fetal Stomach	stomach
40	chr1:184024600-184028800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:184024600-184028800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:184024600-184028800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:184024600-184028800	Weak transcription	Left Ventricle	heart
44	chr1:184024600-184038600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:184024600-184039200	Weak transcription	Lung	lung
46	chr1:184024600-184043800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:184024600-184044400	Weak transcription	Ovary	ovary
48	chr1:184024600-184063400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:184024600-184069400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:184024600-184079400	Weak transcription	Thymus	Thymus

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