Variant report

Variant	rs3129073
Chromosome Location	chr6:29615822-29615823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29598640..29604637-chr6:29614654..29620933,9	K562	blood:
2	chr6:29615478..29616411-chr6:29663958..29664983,4	MCF-7	breast:
3	chr6:29598560..29601918-chr6:29614006..29619393,6	K562	blood:
4	chr6:29615212..29617400-chr6:29662195..29664604,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction
ENSG00000235238	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	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29228	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094579	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3094725	0.80[EUR][1000 genomes]
rs3095266	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3095269	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3095271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095284	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3095290	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3095294	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117289	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117295	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3117299	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3117301	0.81[ASN][1000 genomes]
rs3117312	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3117318	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129039	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129058	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129062	0.93[ASN][1000 genomes]
rs3129063	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129069	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129084	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3129092	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130251	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131895	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131898	0.90[AFR][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	0.90[AFR][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	nsv527037	chr6:29615822-29624112	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3129073	HIST1H3I	cis	cerebellum	SCAN
rs3129073	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3129073	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3129073	BTN3A3	cis	parietal	SCAN
rs3129073	ZKSCAN3	cis	parietal	SCAN
rs3129073	ZFP57	cis	lymphoblastoid	seeQTL
rs3129073	ZNF323	cis	parietal	SCAN
rs3129073	HIST1H2BM	cis	cerebellum	SCAN
rs3129073	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3129073	NKAPL	cis	parietal	SCAN
rs3129073	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29608400-29616400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:29609600-29617200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:29610000-29617200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:29610600-29617200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:29610600-29617400	Weak transcription	K562	blood
6	chr6:29610800-29617200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:29611400-29616800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:29612000-29616800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:29615400-29616000	Enhancers	NHEK	skin
10	chr6:29615800-29616200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:29615800-29616600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:29615800-29616600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:29615800-29617200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:29615800-29617200	Weak transcription	HMEC	breast
15	chr6:29615800-29617400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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