Variant report

Variant	rs3094064
Chromosome Location	chr6:30296253-30296254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr6:30296201-30296471	K562	blood:	n/a	n/a
2	IRF1	chr6:30296238-30296489	K562	blood:	n/a	n/a
3	POLR2A	chr6:30292758-30296347	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:30293079-30296412	IMR90	lung:	n/a	n/a
5	MXI1	chr6:30292693-30296306	IMR90	lung:	n/a	n/a
6	GATA1	chr6:30296053-30296644	PBDE	blood:	n/a	chr6:30296112-30296129

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30225449..30228967-chr6:30292795..30296377,4	K562	blood:
2	chr6:30293058..30297784-chr6:30308514..30315279,24	MCF-7	breast:

Variant related genes	Relation type
TRIM39-RPP21	TF binding region
HCG18	TF binding region
HCG17	TF binding region
TRIM39	TF binding region
ENSG00000243753	Chromatin interaction
ENSG00000241370	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11158	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1264622	0.85[AFR][1000 genomes]
rs1573296	0.81[EUR][1000 genomes]
rs1970	0.81[EUR][1000 genomes]
rs2106072	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2157678	0.81[EUR][1000 genomes]
rs2517609	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2517617	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2517622	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2523712	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2523729	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2844777	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3094054	0.98[EUR][1000 genomes]
rs3094056	0.98[EUR][1000 genomes]
rs3094057	0.98[EUR][1000 genomes]
rs3094058	0.98[EUR][1000 genomes]
rs3094066	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3094067	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094069	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3094078	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3094620	0.98[EUR][1000 genomes]
rs3094621	0.87[EUR][1000 genomes]
rs3094622	0.87[EUR][1000 genomes]
rs3094624	0.98[EUR][1000 genomes]
rs3094625	0.98[EUR][1000 genomes]
rs3094628	0.91[EUR][1000 genomes]
rs3129815	0.98[EUR][1000 genomes]
rs3129830	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130350	0.98[EUR][1000 genomes]
rs3130351	0.98[EUR][1000 genomes]
rs3130352	0.98[EUR][1000 genomes]
rs3130353	0.98[EUR][1000 genomes]
rs3130355	1.00[EUR][1000 genomes]
rs3130363	0.85[EUR][1000 genomes]
rs3130364	0.98[EUR][1000 genomes]
rs3130377	0.98[EUR][1000 genomes]
rs3130380	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130399	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132647	0.98[EUR][1000 genomes]
rs3132648	0.98[EUR][1000 genomes]

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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3094064	ZKSCAN3	cis	parietal	SCAN
rs3094064	HLA-A	cis	lymphoblastoid	GTEx
rs3094064	ZNF323	cis	parietal	SCAN
rs3094064	BTN2A1	cis	parietal	SCAN
rs3094064	HIST1H2BM	cis	cerebellum	SCAN
rs3094064	ZNF192	cis	parietal	SCAN
rs3094064	ZNF192	cis	cerebellum	SCAN
rs3094064	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30295400-30297000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:30295400-30297000	Weak transcription	Ovary	ovary
3	chr6:30295400-30297200	Weak transcription	Aorta	Aorta
4	chr6:30295400-30297200	Weak transcription	Left Ventricle	heart
5	chr6:30295400-30303400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:30295400-30309400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:30295600-30296400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:30295600-30296800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:30295600-30296800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:30295600-30296800	Weak transcription	Placenta	Placenta
11	chr6:30295600-30297000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:30295600-30297000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:30295600-30297000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:30295600-30297000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:30295600-30297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:30295600-30297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:30295600-30297000	Weak transcription	HSMM	muscle
18	chr6:30295600-30297200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:30295600-30297200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:30295600-30297200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:30295600-30297200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:30295600-30297200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:30295600-30297200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:30295600-30297200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:30295600-30297200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:30295600-30297200	Weak transcription	Esophagus	oesophagus
27	chr6:30295600-30297200	Weak transcription	Fetal Intestine Large	intestine
28	chr6:30295600-30297200	Weak transcription	Fetal Thymus	thymus
29	chr6:30295600-30297200	Weak transcription	Gastric	stomach
30	chr6:30295600-30297200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:30295600-30297200	Weak transcription	Spleen	Spleen
32	chr6:30295600-30297200	Weak transcription	HSMMtube	muscle
33	chr6:30295600-30297400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:30295600-30299400	Weak transcription	Stomach Mucosa	stomach
35	chr6:30295600-30301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:30295600-30303400	Weak transcription	Psoas Muscle	Psoas
37	chr6:30295600-30312600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:30295600-30312600	Weak transcription	Right Atrium	heart
39	chr6:30295600-30313000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:30295800-30296400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr6:30295800-30296400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr6:30295800-30296400	Enhancers	Dnd41	blood
43	chr6:30295800-30296400	Enhancers	HepG2	liver
44	chr6:30295800-30296800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:30295800-30296800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:30295800-30296800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:30295800-30296800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:30295800-30296800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:30295800-30296800	Weak transcription	Fetal Brain Female	brain
50	chr6:30295800-30296800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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