Variant report

Variant	rs1264297
Chromosome Location	chr6:30884806-30884807
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30884590-30884949	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30883403..30884976-chr6:30908264..30911485,3	MCF-7	breast:
2	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
3	chr6:30882042..30885135-chr6:30886350..30889389,4	MCF-7	breast:
4	chr6:30881968..30885056-chr6:30885339..30888267,3	MCF-7	breast:
5	chr6:30854396..30859063-chr6:30880954..30884819,5	K562	blood:

No data

Variant related genes	Relation type
VARS2	TF binding region
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000168631	Chromatin interaction
ENSG00000264594	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
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]
rs1264307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:8 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1264297	GRM4	cis	parietal	SCAN
rs1264297	VARS2	cis	multi-tissue	Pritchard
rs1264297	HCG22	cis	lymphoblastoid	seeQTL
rs1264297	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL
rs1264297	HIST1H2BL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30882600-30885000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:30882600-30885000	Enhancers	Lung	lung
3	chr6:30882600-30886800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:30882800-30890200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:30882800-30890200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:30883000-30885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:30883000-30889000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:30883200-30885400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:30883200-30888400	Weak transcription	Small Intestine	intestine
10	chr6:30883400-30887400	Weak transcription	Primary B cells from cord blood	blood
11	chr6:30883400-30887400	Weak transcription	HSMMtube	muscle
12	chr6:30883400-30891200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:30883400-30894400	Weak transcription	Hela-S3	cervix
14	chr6:30883400-30895800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:30883400-30897000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:30883600-30890800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:30883600-30892000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:30883800-30885000	Weak transcription	Gastric	stomach
19	chr6:30883800-30885000	Genic enhancers	HepG2	liver
20	chr6:30883800-30885200	Weak transcription	Right Ventricle	heart
21	chr6:30883800-30885600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:30883800-30886600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:30883800-30887400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:30883800-30889800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:30883800-30889800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:30883800-30890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:30883800-30890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:30883800-30894000	Weak transcription	Fetal Kidney	kidney
29	chr6:30883800-30894200	Weak transcription	Psoas Muscle	Psoas
30	chr6:30883800-30895200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:30883800-30895800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:30883800-30896600	Strong transcription	Fetal Muscle Leg	muscle
33	chr6:30884000-30885000	Weak transcription	Left Ventricle	heart
34	chr6:30884000-30885200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:30884000-30885200	Strong transcription	K562	blood
36	chr6:30884000-30885400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:30884000-30885600	Genic enhancers	Brain Cingulate Gyrus	brain
38	chr6:30884000-30885800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr6:30884000-30885800	Genic enhancers	Dnd41	blood
40	chr6:30884000-30888200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:30884000-30888400	Weak transcription	NHDF-Ad	bronchial
42	chr6:30884000-30889600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:30884000-30889600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:30884000-30890000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:30884000-30890200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr6:30884000-30891600	Strong transcription	Colon Smooth Muscle	Colon
47	chr6:30884000-30894800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr6:30884000-30894800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:30884000-30895000	Strong transcription	Placenta	Placenta
50	chr6:30884000-30895800	Strong transcription	Fetal Muscle Trunk	muscle

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