Variant report

Variant	rs1264319
Chromosome Location	chr6:30862423-30862424
allele	A/G
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	chr6:30862363-30862525	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:30862245-30862446	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:30862407-30862444	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30861872..30865234-chr6:30873633..30877003,5	MCF-7	breast:
2	chr6:30709658..30711296-chr6:30861145..30862930,2	MCF-7	breast:
3	chr6:30860099..30863681-chr6:30886781..30890707,3	K562	blood:
4	chr6:30747932..30749847-chr6:30861062..30862984,2	K562	blood:

Variant related genes	Relation type
DDR1	TF binding region
ENSG00000213780	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000264731	Chromatin interaction
ENSG00000272273	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10947109	0.84[ASN][1000 genomes]
rs11753326	0.81[ASN][1000 genomes]
rs11759918	0.89[ASN][1000 genomes]
rs1264318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189749	0.84[ASN][1000 genomes]
rs17840009	0.89[ASN][1000 genomes]
rs2517576	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535333	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844657	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844659	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2894054	0.86[ASN][1000 genomes]
rs45627239	0.84[ASN][1000 genomes]
rs55697712	0.84[ASN][1000 genomes]
rs59124304	0.84[ASN][1000 genomes]
rs6940037	0.84[ASN][1000 genomes]
rs73727104	0.84[ASN][1000 genomes]
rs73727106	0.84[ASN][1000 genomes]
rs73727107	0.92[ASN][1000 genomes]
rs73727480	0.81[ASN][1000 genomes]
rs7761138	0.92[ASN][1000 genomes]
rs7772269	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv884111	chr6:30845563-30864279	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	nsv884112	chr6:30845563-30866618	Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv884114	chr6:30846830-30867830	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
10	nsv884116	chr6:30848253-30864279	Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884117	chr6:30849124-30862423	Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
12	nsv884120	chr6:30849822-30864279	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
13	nsv884123	chr6:30850191-30865904	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
14	nsv884124	chr6:30854090-30864279	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	18 gene(s)	inside rSNPs	diseases
15	nsv884125	chr6:30854090-30864829	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	18 gene(s)	inside rSNPs	diseases
16	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1264319	C6orf1	cis	parietal	SCAN
rs1264319	HIST1H2AM	cis	cerebellum	SCAN
rs1264319	VARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30854600-30875400	Weak transcription	Psoas Muscle	Psoas
2	chr6:30854800-30862600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:30854800-30862600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:30854800-30870000	Weak transcription	Primary B cells from cord blood	blood
5	chr6:30854800-30875200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:30854800-30875400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:30855000-30868600	Strong transcription	Fetal Intestine Small	intestine
8	chr6:30855600-30868200	Strong transcription	Fetal Intestine Large	intestine
9	chr6:30856000-30867600	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr6:30856000-30868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:30856000-30869200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:30856200-30867800	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr6:30856200-30868000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:30856400-30867400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:30856400-30867800	Strong transcription	Colonic Mucosa	Colon
16	chr6:30856400-30868200	Strong transcription	Primary T cells from cord blood	blood
17	chr6:30856400-30868200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr6:30856400-30868200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:30856400-30868400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:30856600-30863600	Weak transcription	Hela-S3	cervix
21	chr6:30856600-30867600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr6:30856600-30867600	Strong transcription	HepG2	liver
23	chr6:30856600-30867800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr6:30856600-30867800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:30856600-30867800	Strong transcription	Lung	lung
26	chr6:30856600-30867800	Strong transcription	Ovary	ovary
27	chr6:30856600-30868000	Strong transcription	Dnd41	blood
28	chr6:30856600-30868200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:30856600-30868200	Strong transcription	Placenta	Placenta
30	chr6:30856800-30863000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:30856800-30867400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:30856800-30867600	Strong transcription	Adipose Nuclei	Adipose
33	chr6:30856800-30868200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:30857000-30867800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:30857000-30867800	Strong transcription	Spleen	Spleen
36	chr6:30857000-30868200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:30857200-30867600	Strong transcription	Fetal Lung	lung
38	chr6:30857200-30867800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:30857800-30867600	Strong transcription	Pancreas	Pancrea
40	chr6:30858200-30864200	Weak transcription	GM12878-XiMat	blood
41	chr6:30858200-30868200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:30858200-30869000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:30858400-30867400	Strong transcription	Colon Smooth Muscle	Colon
44	chr6:30858400-30867800	Strong transcription	Thymus	Thymus
45	chr6:30858400-30868200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:30858400-30868200	Strong transcription	Gastric	stomach
47	chr6:30858400-30868600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:30858400-30875400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:30858400-30875400	Weak transcription	Right Atrium	heart
50	chr6:30858400-30876000	Weak transcription	Fetal Heart	heart

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