Variant report

Variant	rs916920
Chromosome Location	chr6:30877202-30877203
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30796384..30798794-chr6:30876100..30879027,2	MCF-7	breast:
2	chr6:30849687..30852078-chr6:30875212..30877587,2	K562	blood:
3	chr6:30707481..30713943-chr6:30872979..30880006,10	MCF-7	breast:
4	chr6:30581497..30584727-chr6:30876949..30882098,5	K562	blood:
5	chr6:30710715..30713404-chr6:30876430..30878574,2	K562	blood:
6	chr6:30850512..30853465-chr6:30873614..30877587,4	K562	blood:
7	chr6:30848838..30854096-chr6:30874501..30878794,8	MCF-7	breast:
8	chr6:30862733..30867301-chr6:30870947..30877299,8	K562	blood:
9	chr6:30855370..30857666-chr6:30876080..30878565,2	MCF-7	breast:
10	chr6:30853891..30856446-chr6:30875282..30877202,3	K562	blood:
11	chr6:30521879..30524871-chr6:30874411..30877273,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000222894	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000272273	Chromatin interaction

Extended variants
information (count: 74 )
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];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]
rs1419693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs916920	VARS2	cis	lymphoblastoid	seeQTL
rs916920	HIST1H2BJ	cis	parietal	SCAN
rs916920	ZKSCAN4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30876400-30877400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:30876400-30877400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:30876400-30877400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:30876400-30877400	Flanking Active TSS	Dnd41	blood
5	chr6:30876600-30877400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:30876800-30877400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:30876800-30877400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:30876800-30877400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:30876800-30877400	Enhancers	Brain Substantia Nigra	brain
10	chr6:30876800-30877400	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr6:30876800-30877400	Enhancers	Pancreas	Pancrea
12	chr6:30876800-30877400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr6:30876800-30877400	Enhancers	Right Ventricle	heart
14	chr6:30876800-30877400	Enhancers	HUVEC	blood vessel
15	chr6:30876800-30877400	Enhancers	NHDF-Ad	bronchial
16	chr6:30876800-30877600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:30876800-30877800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:30876800-30878400	Weak transcription	Primary B cells from cord blood	blood
19	chr6:30876800-30878400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:30876800-30881000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:30876800-30881400	Weak transcription	Right Atrium	heart
22	chr6:30876800-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:30876800-30881800	Weak transcription	Small Intestine	intestine
24	chr6:30877000-30877400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:30877000-30877400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:30877000-30877400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:30877000-30877400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:30877000-30877400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:30877000-30877400	Enhancers	Liver	Liver
30	chr6:30877000-30877400	Enhancers	Brain Angular Gyrus	brain
31	chr6:30877000-30877400	Enhancers	Brain Hippocampus Middle	brain
32	chr6:30877000-30877400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr6:30877000-30877400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:30877000-30877400	Enhancers	Colon Smooth Muscle	Colon
35	chr6:30877000-30877400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr6:30877000-30877400	Genic enhancers	Fetal Stomach	stomach
37	chr6:30877000-30877400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:30877000-30877400	Enhancers	GM12878-XiMat	blood
39	chr6:30877000-30877400	Enhancers	HMEC	breast
40	chr6:30877000-30877400	Weak transcription	HSMMtube	muscle
41	chr6:30877000-30877400	Enhancers	NHEK	skin
42	chr6:30877000-30877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:30877000-30877600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:30877000-30877600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:30877000-30877600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:30877000-30877600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:30877000-30877600	Enhancers	Adipose Nuclei	Adipose
48	chr6:30877000-30877600	Weak transcription	Esophagus	oesophagus
49	chr6:30877000-30877600	Enhancers	Fetal Brain Female	brain
50	chr6:30877000-30877600	Weak transcription	Gastric	stomach

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