Variant report

Variant	rs1264307
Chromosome Location	chr6:30880757-30880758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30880670-30881232	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:30880674-30880975	HepG2	liver:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30847750..30851239-chr6:30880214..30883075,5	K562	blood:
2	chr6:30850549..30855941-chr6:30880357..30883667,13	MCF-7	breast:
3	chr6:30793814..30798702-chr6:30880453..30884092,5	K562	blood:
4	chr6:30652620..30655426-chr6:30879070..30880921,2	K562	blood:
5	chr6:30682386..30686066-chr6:30878897..30882722,4	K562	blood:
6	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
7	chr6:30581497..30584727-chr6:30876949..30882098,5	K562	blood:
8	chr6:30583221..30584727-chr6:30879043..30881958,2	K562	blood:
9	chr6:30583713..30586617-chr6:30879172..30881064,2	MCF-7	breast:
10	chr6:30684320..30686534-chr6:30879167..30882068,2	MCF-7	breast:
11	chr6:30880736..30883349-chr6:30890122..30892611,2	MCF-7	breast:
12	chr6:30843411..30845774-chr6:30879579..30881795,2	MCF-7	breast:
13	chr6:30850840..30855328-chr6:30877838..30882665,10	MCF-7	breast:
14	chr6:30844121..30846194-chr6:30880539..30883879,3	K562	blood:
15	chr6:30735539..30738504-chr6:30880365..30881967,2	MCF-7	breast:
16	chr6:30843383..30845810-chr6:30880379..30882936,3	K562	blood:
17	chr6:30583267..30585351-chr6:30880366..30882119,2	MCF-7	breast:
18	chr6:30707880..30713865-chr6:30880456..30883497,7	MCF-7	breast:
19	chr6:30683565..30685674-chr6:30879957..30882271,2	K562	blood:

No data

Variant related genes	Relation type
VARS2	TF binding region
ENSG00000237775	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000214894	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1264297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1264301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264305	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1264320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264342	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17189763	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2074506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240804	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2249459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517449	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517457	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517463	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2517466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517468	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517573	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517575	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517577	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517582	0.86[EUR][1000 genomes]
rs2532920	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532921	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2532928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2532929	0.90[EUR][1000 genomes]
rs2532930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2532933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2532935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2532936	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2532943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535325	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535326	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2535327	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535329	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535330	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535331	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535335	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535336	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535337	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535339	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844654	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844655	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2844658	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844662	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844663	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844664	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844698	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2844699	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2844702	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130657	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7738138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9262288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262291	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1264307	HIST1H2BL	cis	parietal	SCAN
rs1264307	GRM4	cis	parietal	SCAN
rs1264307	VARSL	cis	normal skin	skin_eQTL
rs1264307	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL
rs1264307	VARS2	cis	multi-tissue	Pritchard
rs1264307	HCG22	cis	lymphoblastoid	seeQTL
rs1264307	VARSL	cis	uninvolved skin	skin_eQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30876800-30881000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30876800-30881400	Weak transcription	Right Atrium	heart
3	chr6:30876800-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:30876800-30881800	Weak transcription	Small Intestine	intestine
5	chr6:30877000-30881000	Weak transcription	Psoas Muscle	Psoas
6	chr6:30877000-30881200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:30877000-30881200	Weak transcription	Fetal Heart	heart
8	chr6:30877000-30881200	Weak transcription	Stomach Mucosa	stomach
9	chr6:30877000-30881200	Weak transcription	A549	lung
10	chr6:30877000-30881400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:30877200-30880800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:30877200-30881000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:30877200-30881000	Weak transcription	Fetal Brain Male	brain
14	chr6:30877200-30881000	Strong transcription	Fetal Intestine Large	intestine
15	chr6:30877200-30881000	Strong transcription	Fetal Intestine Small	intestine
16	chr6:30877200-30881200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:30877200-30881200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:30877200-30881200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:30877200-30881200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:30877200-30881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:30877200-30881400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:30877200-30881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:30877200-30881400	Weak transcription	HSMM	muscle
24	chr6:30877400-30880800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:30877400-30880800	Strong transcription	HSMMtube	muscle
26	chr6:30877400-30881000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr6:30877400-30881000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:30877400-30881200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:30877400-30881400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:30877400-30881400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:30877400-30881400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:30877400-30881400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:30877400-30881400	Strong transcription	Fetal Stomach	stomach
34	chr6:30877400-30881600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:30877400-30881600	Strong transcription	K562	blood
36	chr6:30877600-30880800	Strong transcription	Placenta	Placenta
37	chr6:30877600-30880800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr6:30877600-30880800	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:30877600-30880800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr6:30877600-30881000	Strong transcription	NHLF	lung
41	chr6:30877600-30881200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:30877600-30881200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:30877600-30881200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:30877600-30881200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:30877600-30881200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:30877600-30881200	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:30877600-30881400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:30877600-30881400	Strong transcription	Osteobl	bone
49	chr6:30877800-30881000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:30877800-30881000	Strong transcription	Brain Germinal Matrix	brain

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