Variant report

Variant	rs3117289
Chromosome Location	chr6:29609921-29609922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29608179..29610477-chr6:29617988..29619609,2	K562	blood:
2	chr6:29609140..29610048-chr6:29673773..29674677,2	MCF-7	breast:
3	chr6:29598626..29603210-chr6:29607516..29611410,5	K562	blood:
4	chr6:29609719..29612322-chr6:29612804..29614354,2	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs2535238	0.93[ASN][1000 genomes]
rs2535274	0.81[ASN][1000 genomes]
rs2535275	0.81[ASN][1000 genomes]
rs2747421	0.93[ASN][1000 genomes]
rs2747427	0.93[ASN][1000 genomes]
rs2747428	0.93[ASN][1000 genomes]
rs2747429	0.93[ASN][1000 genomes]
rs2747460	0.81[ASN][1000 genomes]
rs2907897	0.81[ASN][1000 genomes]
rs29218	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29228	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094579	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3094725	0.80[EUR][1000 genomes]
rs3095266	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3095269	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3095271	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095284	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3095290	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3095294	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117295	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3117299	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3117301	0.81[ASN][1000 genomes]
rs3117312	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3117318	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129039	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129058	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129062	0.93[ASN][1000 genomes]
rs3129063	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129069	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129073	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129084	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3129092	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130251	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131895	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131898	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs374317	0.93[ASN][1000 genomes]
rs375248	0.92[ASN][1000 genomes]
rs375984	0.93[ASN][1000 genomes]
rs376319	0.93[ASN][1000 genomes]
rs387640	0.93[ASN][1000 genomes]
rs387642	0.93[ASN][1000 genomes]
rs417764	0.93[ASN][1000 genomes]
rs448380	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs448489	0.93[ASN][1000 genomes]
rs9258017	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv969292	chr6:29604881-29612154	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3117289	NKAPL	cis	parietal	SCAN
rs3117289	ZFP57	cis	lymphoblastoid	seeQTL
rs3117289	HIST1H2BM	cis	cerebellum	SCAN
rs3117289	HIST1H3I	cis	cerebellum	SCAN
rs3117289	BTN3A3	cis	parietal	SCAN
rs3117289	ZNF323	cis	parietal	SCAN
rs3117289	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs3117289	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3117289	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3117289	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3117289	ZKSCAN3	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29608400-29610600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:29608400-29610800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:29608400-29611000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:29608400-29611600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr6:29608400-29616400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:29608600-29610000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:29608600-29610200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr6:29608600-29610400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr6:29608800-29610400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:29608800-29611200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:29609200-29610000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:29609200-29610000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:29609200-29610000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:29609200-29610000	Enhancers	GM12878-XiMat	blood
15	chr6:29609200-29610000	Enhancers	Hela-S3	cervix
16	chr6:29609200-29610000	Enhancers	HMEC	breast
17	chr6:29609200-29610000	Enhancers	NHEK	skin
18	chr6:29609200-29610200	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:29609200-29610200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:29609200-29610200	Enhancers	Stomach Mucosa	stomach
21	chr6:29609200-29610400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr6:29609400-29610000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr6:29609400-29610000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr6:29609400-29610000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:29609400-29610200	Enhancers	Primary B cells from cord blood	blood
26	chr6:29609600-29610000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:29609600-29610000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:29609600-29610000	Enhancers	A549	lung
29	chr6:29609600-29610000	Flanking Active TSS	K562	blood
30	chr6:29609600-29610200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:29609600-29617200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:29609800-29610000	Enhancers	Primary T cells from cord blood	blood
33	chr6:29609800-29610000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr6:29609800-29610800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr6:29609800-29615600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:29609800-29615600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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