Variant report

Variant	rs2816329
Chromosome Location	chr1:226166497-226166498
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226164266..226167338-chr1:226248609..226251593,3	MCF-7	breast:
2	chr1:226165753..226166698-chr1:226309249..226309754,2	K562	blood:
3	chr1:226163855..226167681-chr1:226167885..226170495,3	K562	blood:
4	chr1:226166138..226168581-chr1:226249568..226252466,2	K562	blood:
5	chr1:226028800..226031173-chr1:226165446..226167469,2	MCF-7	breast:
6	chr1:226165055..226167554-chr1:226173060..226175122,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10915916	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2180421	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2475152	0.88[CEU][hapmap]
rs2749698	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2816330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653701	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653702	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426091	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426092	0.87[EUR][1000 genomes]
rs6657197	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6664468	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6690247	0.85[EUR][1000 genomes];0.93[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	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2816329	MOSC1	cis	cerebellum	SCAN
rs2816329	IARS2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226129600-226185600	Weak transcription	Right Atrium	heart
2	chr1:226156800-226167200	Weak transcription	HepG2	liver
3	chr1:226156800-226167600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:226157000-226167200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:226157000-226167400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:226161200-226167200	Weak transcription	Fetal Kidney	kidney
7	chr1:226161200-226167200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:226162400-226173000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:226163200-226167200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:226163600-226175800	Weak transcription	Aorta	Aorta
11	chr1:226163800-226167200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:226163800-226167200	Weak transcription	A549	lung
13	chr1:226163800-226167200	Weak transcription	NHLF	lung
14	chr1:226163800-226167400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:226163800-226167400	Weak transcription	Dnd41	blood
16	chr1:226163800-226167400	Weak transcription	HUVEC	blood vessel
17	chr1:226163800-226167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:226163800-226167600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:226163800-226167600	Weak transcription	NH-A	brain
20	chr1:226163800-226167800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:226163800-226167800	Weak transcription	NHDF-Ad	bronchial
22	chr1:226163800-226168200	Weak transcription	Psoas Muscle	Psoas
23	chr1:226163800-226169000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:226163800-226169000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:226163800-226169000	Weak transcription	HMEC	breast
26	chr1:226163800-226174400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:226163800-226175400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:226163800-226175600	Weak transcription	Gastric	stomach
29	chr1:226163800-226175800	Weak transcription	Esophagus	oesophagus
30	chr1:226163800-226178800	Weak transcription	Right Ventricle	heart
31	chr1:226164000-226167400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:226164000-226167400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:226164000-226167400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:226164000-226167400	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:226164000-226167400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:226164000-226167600	Weak transcription	Stomach Mucosa	stomach
37	chr1:226164000-226169000	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:226164000-226171200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:226164000-226171200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:226164000-226172800	Weak transcription	Brain Substantia Nigra	brain
41	chr1:226164200-226167400	Weak transcription	Fetal Brain Female	brain
42	chr1:226164200-226171200	Weak transcription	Brain Angular Gyrus	brain
43	chr1:226164400-226166800	Enhancers	Primary B cells from cord blood	blood
44	chr1:226164400-226167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:226164400-226169000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:226164400-226179000	Weak transcription	Small Intestine	intestine
47	chr1:226164600-226167400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:226164600-226169000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:226164600-226169000	Strong transcription	Fetal Stomach	stomach
50	chr1:226164600-226169800	Strong transcription	Thymus	Thymus

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