Variant report

Variant	rs9380069
Chromosome Location	chr6:28203300-28203301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28202355..28207419-chr6:28302691..28306303,4	K562	blood:
2	chr6:28201636..28204164-chr6:28301226..28303340,2	K562	blood:
3	chr6:28201634..28205338-chr6:28303433..28306544,4	K562	blood:
4	chr6:28202226..28208942-chr6:28209296..28217649,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10456362	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs11755032	0.91[GIH][hapmap]
rs11965538	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs13200462	0.93[CEU][hapmap]
rs1321505	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1339899	0.91[GIH][hapmap]
rs1419183	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs1679709	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs1679732	0.93[CEU][hapmap]
rs17720293	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1778507	1.00[GIH][hapmap]
rs1778508	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs1778511	0.93[CEU][hapmap]
rs1936365	0.91[GIH][hapmap]
rs213241	0.91[GIH][hapmap]
rs213244	0.91[GIH][hapmap]
rs2743554	0.91[GIH][hapmap]
rs2799077	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs2799079	0.93[CEU][hapmap]
rs34130214	0.80[EUR][1000 genomes]
rs34712084	0.80[EUR][1000 genomes]
rs3757188	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs4713139	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs4713140	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs6901575	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs735765	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs8180562	0.80[EUR][1000 genomes]
rs853676	0.91[GIH][hapmap]
rs853679	0.91[GIH][hapmap]
rs853681	0.91[GIH][hapmap]
rs853685	0.91[GIH][hapmap]
rs9366717	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs9368561	0.85[EUR][1000 genomes]
rs9380051	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs9380064	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs9393902	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs9393908	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs9461446	1.00[GIH][hapmap]
rs9461448	0.91[GIH][hapmap]
rs9468287	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs9468300	0.80[EUR][1000 genomes]
rs9468322	1.00[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs9380069		cis	Lymphoblastoid	GTEx
rs9380069	LOC222699	cis	lymphoblastoid	seeQTL
rs9380069	AL022393.7	cis	Muscle Skeletal	GTEx
rs9380069	ABT1	cis	parietal	SCAN
rs9380069	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9380069	HIST1H4L	cis	parietal	SCAN
rs9380069	HLA-A	cis	multi-tissue	Pritchard
rs9380069	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9380069	ZNF323	cis	parietal	SCAN
rs9380069	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs9380069	BTN3A2	cis	multi-tissue	Pritchard
rs9380069	ZSCAN23	cis	cerebellum	SCAN
rs9380069	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9380069	ZNF192	cis	cerebellum	SCAN
rs9380069	ZSCAN23	cis	parietal	SCAN
rs9380069	LRRC16A	cis	parietal	SCAN
rs9380069	BTN3A2	trans	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193600-28213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:28193800-28204000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28193800-28211800	Weak transcription	Fetal Thymus	thymus
4	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
6	chr6:28194000-28211000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:28194000-28211800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:28194000-28212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:28194000-28213000	Weak transcription	Thymus	Thymus
10	chr6:28194000-28213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:28194600-28207000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:28194800-28204200	Strong transcription	Left Ventricle	heart
13	chr6:28194800-28205000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:28195000-28203800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:28195200-28204600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:28195400-28204600	Strong transcription	Placenta	Placenta
17	chr6:28196600-28203400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:28196600-28203400	Strong transcription	Fetal Brain Female	brain
19	chr6:28196800-28203400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:28196800-28212400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:28196800-28212400	Weak transcription	Small Intestine	intestine
22	chr6:28196800-28213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:28197000-28212400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:28197600-28203600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:28198800-28212200	Weak transcription	Hela-S3	cervix
26	chr6:28199200-28213200	Weak transcription	Colonic Mucosa	Colon
27	chr6:28199800-28213600	Weak transcription	NHDF-Ad	bronchial
28	chr6:28200400-28212400	Weak transcription	Fetal Intestine Small	intestine
29	chr6:28200400-28212600	Weak transcription	NHEK	skin
30	chr6:28200800-28212400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:28200800-28212600	Weak transcription	Fetal Heart	heart
32	chr6:28201000-28203600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:28201000-28206400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:28201000-28211000	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:28201000-28211600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:28201000-28212200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:28201000-28212200	Weak transcription	Brain Anterior Caudate	brain
38	chr6:28201000-28212400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:28201000-28212400	Weak transcription	HMEC	breast
40	chr6:28201000-28212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:28201000-28212800	Weak transcription	Pancreas	Pancrea
42	chr6:28201000-28212800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:28201000-28212800	Weak transcription	Right Ventricle	heart
44	chr6:28201200-28206000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:28201200-28206400	Weak transcription	Ovary	ovary
46	chr6:28201200-28212200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:28201400-28206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:28201600-28203800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:28201600-28206400	Weak transcription	Lung	lung
50	chr6:28201600-28211600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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