Variant report

Variant	rs8408
Chromosome Location	chr6:30867666-30867667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30693489..30695264-chr6:30866666..30869392,2	K562	blood:
2	chr6:30863479..30866795-chr6:30867432..30870165,5	MCF-7	breast:
3	chr6:30708211..30712541-chr6:30866148..30872025,6	MCF-7	breast:
4	chr6:30865395..30867795-chr6:30868039..30871871,4	K562	blood:
5	chr6:30867554..30871649-chr6:30872522..30875092,3	MCF-7	breast:
6	chr6:30862088..30864783-chr6:30865589..30868630,4	K562	blood:
7	chr6:30865273..30868219-chr6:30870202..30872766,2	MCF-7	breast:
8	chr6:30710148..30713140-chr6:30864096..30868029,4	MCF-7	breast:
9	chr6:30867305..30868818-chr6:30880725..30882258,2	K562	blood:
10	chr6:30867567..30870508-chr6:30872843..30875711,3	K562	blood:
11	chr6:30582895..30585120-chr6:30867522..30869594,2	MCF-7	breast:
12	chr6:30796461..30798105-chr6:30865985..30868433,2	MCF-7	breast:
13	chr6:30848483..30851183-chr6:30866301..30867885,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000264731	Chromatin interaction
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

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];1.00[ASN][1000 genomes]
rs1049628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12206075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215246	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215409	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074511	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2074512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229933	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239518	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285319	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286655	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2524236	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2894055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213644	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3218802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869085	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3909130	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41288539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4618569	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711247	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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];0.88[ASN][1000 genomes]
rs6457282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901464	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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];0.86[ASN][1000 genomes]
rs6924600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743661	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756521	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295929	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295933	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357102	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366761	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368646	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378191	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380200	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394021	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461638	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468842	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468847	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9501032	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.93[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	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	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
8	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
9	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8408	ZKSCAN4	cis	cerebellum	SCAN
rs8408	VARS2	cis	lymphoblastoid	seeQTL
rs8408	HIST1H2BJ	cis	parietal	SCAN

Chromatin state (count:112 , 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	chr6:30854800-30870000	Weak transcription	Primary B cells from cord blood	blood
3	chr6:30854800-30875200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:30854800-30875400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:30855000-30868600	Strong transcription	Fetal Intestine Small	intestine
6	chr6:30855600-30868200	Strong transcription	Fetal Intestine Large	intestine
7	chr6:30856000-30868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:30856000-30869200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:30856200-30867800	Strong transcription	Placenta Amnion	Placenta Amnion
10	chr6:30856200-30868000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr6:30856400-30867800	Strong transcription	Colonic Mucosa	Colon
12	chr6:30856400-30868200	Strong transcription	Primary T cells from cord blood	blood
13	chr6:30856400-30868200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr6:30856400-30868200	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:30856400-30868400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:30856600-30867800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr6:30856600-30867800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:30856600-30867800	Strong transcription	Lung	lung
19	chr6:30856600-30867800	Strong transcription	Ovary	ovary
20	chr6:30856600-30868000	Strong transcription	Dnd41	blood
21	chr6:30856600-30868200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:30856600-30868200	Strong transcription	Placenta	Placenta
23	chr6:30856800-30868200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:30857000-30867800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:30857000-30867800	Strong transcription	Spleen	Spleen
26	chr6:30857000-30868200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:30857200-30867800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:30858200-30868200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:30858200-30869000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:30858400-30867800	Strong transcription	Thymus	Thymus
31	chr6:30858400-30868200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:30858400-30868200	Strong transcription	Gastric	stomach
33	chr6:30858400-30868600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:30858400-30875400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:30858400-30875400	Weak transcription	Right Atrium	heart
36	chr6:30858400-30876000	Weak transcription	Fetal Heart	heart
37	chr6:30858600-30868200	Strong transcription	Brain Germinal Matrix	brain
38	chr6:30858600-30868200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:30858600-30868200	Strong transcription	Esophagus	oesophagus
40	chr6:30858600-30868200	Strong transcription	HSMMtube	muscle
41	chr6:30858600-30868400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:30858600-30868600	Strong transcription	Fetal Stomach	stomach
43	chr6:30858600-30869000	Strong transcription	NHEK	skin
44	chr6:30858600-30875200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:30858800-30868400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:30858800-30868600	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:30858800-30875200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:30859000-30868200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:30859000-30869000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:30859200-30867800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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