Variant report

Variant	rs1419693
Chromosome Location	chr6:30877760-30877761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30877746-30877796	HCM	heart:	n/a
2	chr6:30877739-30877789	SAEC	small airway:	n/a
3	chr6:30877746-30877796	HUVEC	blood vessel:	n/a
4	chr6:30877739-30877789	Caco-2	colon:	n/a
5	chr6:30877739-30877789	HEEpiC	esophagus:	n/a
6	chr6:30877739-30877789	PrEC	prostate:	n/a
7	chr6:30877746-30877796	HCT-116	colon:	n/a
8	chr6:30877746-30877796	PANC-1	pancreas:	n/a
9	chr6:30877746-30877796	HL-60	blood:	n/a
10	chr6:30877739-30877789	U87	brain:	n/a
11	chr6:30877739-30877789	HL-60	blood:	n/a
12	chr6:30877746-30877796	GM19239	blood:	n/a
13	chr6:30877746-30877796	BE2_C	brain:	n/a
14	chr6:30877739-30877789	HRE	kidney:	n/a
15	chr6:30877746-30877796	HCF	heart:	n/a
16	chr6:30877746-30877796	GM12891	blood:	n/a
17	chr6:30877739-30877789	NT2-D1	testis:	n/a
18	chr6:30877739-30877789	Jurkat	blood:	n/a
19	chr6:30877746-30877796	AG04450	lung:	fetal
20	chr6:30877746-30877796	T-47D	breast:	n/a
21	chr6:30877739-30877789	H1-hESC	embryonic stem cell:	embryo
22	chr6:30877739-30877789	BE2_C	brain:	n/a
23	chr6:30877746-30877796	NHDF-neo	bronchial:	n/a
24	chr6:30877739-30877789	LNCaP	prostate:	n/a
25	chr6:30877739-30877789	AG04450	lung:	fetal
26	chr6:30877739-30877789	Hela-S3	cervix:	n/a
27	chr6:30877746-30877796	MCF10A-Er-Src	breast:	n/a
28	chr6:30877739-30877789	HNPCEpiC	eye:	n/a
29	chr6:30877739-30877789	MCF-7	breast:	n/a
30	chr6:30877739-30877789	HEK293	kidney:	embryo
31	chr6:30877739-30877789	IMR90	lung:	fetal
32	chr6:30877739-30877789	A549	lung:	n/a
33	chr6:30877746-30877796	SKMC	muscle:	n/a
34	chr6:30877739-30877789	Hepatocyte	liver:	n/a
35	chr6:30877739-30877789	ovcar-3	ovarian:	n/a
36	chr6:30877739-30877789	BJ	skin:	n/a
37	chr6:30877739-30877789	HCT-116	colon:	n/a
38	chr6:30877739-30877789	HCPEpiC	choroid plexus:	n/a
39	chr6:30877739-30877789	GM12892	blood:	n/a
40	chr6:30877739-30877789	HMEC	breast:	n/a
41	chr6:30877739-30877789	HCM	heart:	n/a
42	chr6:30877746-30877796	SK-N-MC	brain:	n/a
43	chr6:30877739-30877789	NB4	blood:	n/a
44	chr6:30877746-30877796	U87	brain:	n/a
45	chr6:30877746-30877796	PrEC	prostate:	n/a
46	chr6:30877739-30877789	SK-N-MC	brain:	n/a
47	chr6:30877739-30877789	PANC-1	pancreas:	n/a
48	chr6:30877739-30877789	HIPEpiC	eye:	n/a
49	chr6:30877746-30877796	Caco-2	colon:	n/a
50	chr6:30877739-30877789	SK-N-SH_RA	brain:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30796384..30798794-chr6:30876100..30879027,2	MCF-7	breast:
2	chr6:30707481..30713943-chr6:30872979..30880006,10	MCF-7	breast:
3	chr6:30581497..30584727-chr6:30876949..30882098,5	K562	blood:
4	chr6:30710715..30713404-chr6:30876430..30878574,2	K562	blood:
5	chr6:30848838..30854096-chr6:30874501..30878794,8	MCF-7	breast:
6	chr6:30831173..30833019-chr6:30877355..30879360,2	K562	blood:
7	chr6:30855370..30857666-chr6:30876080..30878565,2	MCF-7	breast:

No data

Variant related genes	Relation type
VARS2	CpG island
GTF2H4	CpG island
ENSG00000214894	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000202241	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1049622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1049628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12206075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13215246	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13215409	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074511	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2074512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229933	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239518	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2284175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285319	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2286655	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2524236	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2894055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213644	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3218802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3218803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3218806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3218814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3218815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3869085	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3869086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3909130	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41288539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4618569	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711247	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711249	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4713402	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6457282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6901464	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6920760	0.82[EUR][1000 genomes]
rs6921687	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6924600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7743661	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756521	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7761589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs916920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295929	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295933	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357102	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366761	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368646	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9378191	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380200	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394021	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461638	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468842	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468847	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9501032	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9501035	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9501342	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30876800-30877800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:30876800-30878400	Weak transcription	Primary B cells from cord blood	blood
3	chr6:30876800-30878400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:30876800-30881000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:30876800-30881400	Weak transcription	Right Atrium	heart
6	chr6:30876800-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:30876800-30881800	Weak transcription	Small Intestine	intestine
8	chr6:30877000-30877800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:30877000-30877800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr6:30877000-30877800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:30877000-30877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:30877000-30877800	Weak transcription	Lung	lung
13	chr6:30877000-30877800	Weak transcription	Ovary	ovary
14	chr6:30877000-30877800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:30877000-30878000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:30877000-30878200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:30877000-30878200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:30877000-30878400	Weak transcription	Primary T cells from cord blood	blood
19	chr6:30877000-30878400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:30877000-30878400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:30877000-30878600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:30877000-30878600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:30877000-30881000	Weak transcription	Psoas Muscle	Psoas
24	chr6:30877000-30881200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:30877000-30881200	Weak transcription	Fetal Heart	heart
26	chr6:30877000-30881200	Weak transcription	Stomach Mucosa	stomach
27	chr6:30877000-30881200	Weak transcription	A549	lung
28	chr6:30877000-30881400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:30877200-30877800	Weak transcription	Aorta	Aorta
30	chr6:30877200-30877800	Weak transcription	Brain Anterior Caudate	brain
31	chr6:30877200-30877800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:30877200-30877800	Weak transcription	Brain Germinal Matrix	brain
33	chr6:30877200-30877800	Weak transcription	Colonic Mucosa	Colon
34	chr6:30877200-30877800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:30877200-30877800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:30877200-30877800	Weak transcription	Spleen	Spleen
37	chr6:30877200-30877800	Enhancers	HepG2	liver
38	chr6:30877200-30878000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:30877200-30878000	Weak transcription	Fetal Kidney	kidney
40	chr6:30877200-30878400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:30877200-30878400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:30877200-30878400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:30877200-30878400	Weak transcription	NH-A	brain
44	chr6:30877200-30880800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:30877200-30881000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:30877200-30881000	Weak transcription	Fetal Brain Male	brain
47	chr6:30877200-30881000	Strong transcription	Fetal Intestine Large	intestine
48	chr6:30877200-30881000	Strong transcription	Fetal Intestine Small	intestine
49	chr6:30877200-30881200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:30877200-30881200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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