Variant report

Variant	rs885905
Chromosome Location	chr6:30890431-30890432
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	POLR2A	chr6:30889929-30890480	K562	blood:	n/a	n/a
2	FOS	chr6:30890178-30890564	MCF10A-Er-Src	breast:	n/a	chr6:30890553-30890560 chr6:30890552-30890561
3	POLR2A	chr6:30890151-30890781	K562	blood:	n/a	n/a
4	JUND	chr6:30890242-30890704	H1-hESC	embryonic stem cell:	n/a	chr6:30890566-30890575 chr6:30890553-30890560 chr6:30890552-30890561 chr6:30890550-30890561
5	CTCF	chr6:30890400-30890550	GM12864	blood:	n/a	n/a
6	CTCF	chr6:30890360-30890510	MCF-7	breast:	n/a	n/a
7	FOS	chr6:30890203-30890713	MCF10A-Er-Src	breast:	n/a	chr6:30890566-30890575 chr6:30890553-30890560 chr6:30890552-30890561
8	STAT3	chr6:30890356-30890470	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr6:30890244-30890471	NHEK	skin:	n/a	chr6:30890349-30890357
10	FOS	chr6:30890151-30890597	MCF10A-Er-Src	breast:	n/a	chr6:30890566-30890575 chr6:30890553-30890560 chr6:30890552-30890561
11	CTCF	chr6:30890300-30890450	HMEC	breast:	n/a	chr6:30890349-30890357
12	POLR2A	chr6:30889977-30891201	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:30890155-30890432	K562	blood:	n/a	n/a
14	FOSL2	chr6:30890357-30890671	HepG2	liver:	n/a	chr6:30890566-30890575 chr6:30890553-30890560 chr6:30890552-30890561
15	FOS	chr6:30890160-30890629	MCF10A-Er-Src	breast:	n/a	chr6:30890566-30890575 chr6:30890553-30890560 chr6:30890552-30890561
16	CTCF	chr6:30890340-30890490	NHEK	skin:	n/a	chr6:30890349-30890357

No.	Distal block	Cell Line	Cell type
1	chr6:30860099..30863681-chr6:30886781..30890707,3	K562	blood:
2	chr6:30593365..30595936-chr6:30888888..30891859,2	K562	blood:
3	chr6:30880736..30883349-chr6:30890122..30892611,2	MCF-7	breast:
4	chr6:30889584..30892260-chr6:30907683..30910382,2	MCF-7	breast:
5	chr6:30850869..30853262-chr6:30889505..30891289,2	MCF-7	breast:

Variant related genes	Relation type
VARS2	TF binding region
ENSG00000168631	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137343	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1043483	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264306	0.87[ASN][1000 genomes]
rs2253588	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517459	0.81[EUR][1000 genomes]
rs2532925	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2532932	0.81[EUR][1000 genomes]
rs2532941	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv523346	chr6:30882513-30893941	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
9	nsv884126	chr6:30886350-30895990	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs885905	PRSS16	cis	cerebellum	SCAN
rs885905	VARS2	cis	lymphoblastoid	seeQTL
rs885905	HIST1H2AL	cis	cerebellum	SCAN
rs885905	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30883400-30891200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:30883400-30894400	Weak transcription	Hela-S3	cervix
3	chr6:30883400-30895800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:30883400-30897000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:30883600-30890800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:30883600-30892000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:30883800-30894000	Weak transcription	Fetal Kidney	kidney
8	chr6:30883800-30894200	Weak transcription	Psoas Muscle	Psoas
9	chr6:30883800-30895200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:30883800-30895800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:30883800-30896600	Strong transcription	Fetal Muscle Leg	muscle
12	chr6:30884000-30891600	Strong transcription	Colon Smooth Muscle	Colon
13	chr6:30884000-30894800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr6:30884000-30894800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:30884000-30895000	Strong transcription	Placenta	Placenta
16	chr6:30884000-30895800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr6:30884000-30896000	Strong transcription	Fetal Stomach	stomach
18	chr6:30884000-30896200	Strong transcription	Fetal Thymus	thymus
19	chr6:30884000-30897000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:30884200-30893800	Weak transcription	Fetal Brain Male	brain
21	chr6:30884200-30894000	Weak transcription	HSMM	muscle
22	chr6:30884200-30894800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:30884200-30894800	Strong transcription	Fetal Intestine Large	intestine
24	chr6:30884200-30895000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:30884200-30895400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr6:30884200-30895600	Strong transcription	Fetal Intestine Small	intestine
27	chr6:30884200-30896200	Strong transcription	Fetal Brain Female	brain
28	chr6:30884400-30890600	Strong transcription	GM12878-XiMat	blood
29	chr6:30884400-30894600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr6:30884400-30894600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr6:30884400-30894800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:30884400-30894800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:30884400-30894800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:30884400-30894800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr6:30884400-30895000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:30884400-30895000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:30884400-30895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:30884400-30895800	Strong transcription	Primary T cells from cord blood	blood
39	chr6:30884600-30890600	Strong transcription	Spleen	Spleen
40	chr6:30884600-30891600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:30884600-30891800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:30884600-30891800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:30884600-30893400	Strong transcription	Rectal Smooth Muscle	rectum
44	chr6:30884600-30894400	Strong transcription	Osteobl	bone
45	chr6:30884600-30894600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:30884600-30894800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:30884600-30894800	Strong transcription	Adipose Nuclei	Adipose
48	chr6:30884600-30895000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:30884600-30895200	Strong transcription	Thymus	Thymus
50	chr6:30884600-30895400	Strong transcription	Ovary	ovary

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