Variant report

Variant	rs2206061
Chromosome Location	chr22:29175873-29175874
allele	A/G
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	chr22:29172058..29177577-chr22:29178390..29181662,9	MCF-7	breast:
2	chr22:29175268..29177252-chr22:29194903..29197357,4	MCF-7	breast:
3	chr22:29174303..29175888-chr22:29187835..29189460,2	MCF-7	breast:
4	chr22:29165791..29171536-chr22:29171828..29178249,15	MCF-7	breast:
5	chr22:29175785..29179613-chr22:29195586..29198060,4	K562	blood:
6	chr22:29004756..29007074-chr22:29174850..29177158,2	K562	blood:
7	chr22:29174714..29176421-chr22:29187475..29189303,2	K562	blood:
8	chr22:29174755..29176682-chr22:29192335..29194092,2	K562	blood:
9	chr22:29167384..29172904-chr22:29173066..29177227,7	K562	blood:
10	chr22:29175158..29176844-chr22:29194433..29196977,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159873	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10427858	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12165475	0.82[YRI][hapmap]
rs12166716	1.00[YRI][hapmap]
rs12167378	0.82[YRI][hapmap]
rs12330071	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17878936	0.82[YRI][hapmap]
rs2073326	0.82[YRI][hapmap]
rs2228260	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235432	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs41281603	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56119508	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5752839	1.00[MEX][hapmap]
rs5762893	1.00[MEX][hapmap]
rs5762900	1.00[MEX][hapmap]
rs5762906	1.00[MEX][hapmap]
rs5997389	0.89[AFR][1000 genomes]
rs5997390	0.89[AFR][1000 genomes]
rs5997401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005856	0.89[AFR][1000 genomes]
rs6005861	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005868	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6005870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005874	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005923	0.86[EUR][1000 genomes]
rs6005924	0.86[EUR][1000 genomes]
rs6005926	0.86[EUR][1000 genomes]
rs60116790	0.97[AFR][1000 genomes]
rs7288513	1.00[MEX][hapmap]
rs7290364	1.00[MEX][hapmap]
rs73388803	0.89[AFR][1000 genomes]
rs9306460	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9620826	1.00[ASW][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9620828	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9620833	0.89[AFR][1000 genomes]
rs9620839	1.00[YRI][hapmap]
rs9625544	0.82[YRI][hapmap]
rs9625547	0.80[AFR][1000 genomes]
rs9625548	0.94[AFR][1000 genomes]
rs9625551	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625554	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9625562	0.81[AFR][1000 genomes]
rs9625565	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625568	0.97[AFR][1000 genomes]
rs9625572	0.97[AFR][1000 genomes]
rs9625575	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9625580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625645	1.00[MEX][hapmap];0.85[YRI][hapmap]
rs9625657	1.00[MEX][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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2206061	DDX3Y	trans	brain	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29169800-29180000	Weak transcription	Colonic Mucosa	Colon
3	chr22:29169800-29180200	Weak transcription	Stomach Mucosa	stomach
4	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29170000-29176400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr22:29170000-29176400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr22:29170000-29177600	Weak transcription	Aorta	Aorta
8	chr22:29170000-29179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr22:29170000-29179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr22:29170000-29182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
12	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr22:29170200-29177800	Weak transcription	HMEC	breast
14	chr22:29170200-29178000	Weak transcription	Brain Anterior Caudate	brain
15	chr22:29170200-29178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
17	chr22:29170400-29177800	Strong transcription	Fetal Intestine Large	intestine
18	chr22:29170400-29183800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr22:29170400-29184000	Strong transcription	Fetal Muscle Leg	muscle
20	chr22:29170400-29185600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:29170600-29184600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:29170600-29184800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr22:29170600-29185400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr22:29170800-29179800	Weak transcription	Fetal Brain Male	brain
27	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr22:29171000-29176400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr22:29171000-29176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr22:29171000-29178000	Weak transcription	Brain Angular Gyrus	brain
31	chr22:29171000-29179600	Weak transcription	Small Intestine	intestine
32	chr22:29171000-29185600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr22:29171200-29176400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr22:29171200-29177000	Weak transcription	Brain Hippocampus Middle	brain
35	chr22:29171200-29178600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr22:29171200-29179000	Weak transcription	Brain Substantia Nigra	brain
37	chr22:29171200-29179200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:29171200-29186800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr22:29171200-29188600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr22:29171400-29179600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr22:29171400-29186000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr22:29171600-29178000	Weak transcription	Fetal Kidney	kidney
43	chr22:29171800-29178000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr22:29171800-29186200	Strong transcription	Fetal Thymus	thymus
45	chr22:29172000-29179400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr22:29172200-29176600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr22:29172200-29176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr22:29172200-29177800	Weak transcription	Brain Germinal Matrix	brain
49	chr22:29172200-29179600	Weak transcription	NHLF	lung
50	chr22:29172400-29176200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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