Variant report

Variant	rs3888777
Chromosome Location	chr6:30529816-30529817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30529071-30529991	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:30528766-30529893	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr6:30529549-30529820	HCT-116	colon:	n/a	n/a
4	POLR2A	chr6:30529123-30529826	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:30529130-30531355	K562	blood:	n/a	n/a
6	POLR2A	chr6:30529806-30529888	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:30529715-30529880	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:30529063-30529909	K562	blood:	n/a	n/a
9	POLR2A	chr6:30529801-30530075	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:30529590-30532337	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:30529557-30529920	K562	blood:	n/a	n/a
12	POLR2A	chr6:30529521-30529994	K562	blood:	n/a	n/a
13	POLR2A	chr6:30528828-30530093	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:30528616-30532626	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr6:30528704-30532497	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30529541..30531687-chr6:30583397..30586994,3	MCF-7	breast:
2	chr6:30461955..30465538-chr6:30528030..30531365,3	K562	blood:

Variant related genes	Relation type
GNL1	TF binding region
ENSG00000204568	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs16867845	0.83[AMR][1000 genomes]
rs17189120	0.83[AMR][1000 genomes]
rs17189134	0.83[AMR][1000 genomes]
rs17189155	0.83[AMR][1000 genomes]
rs17195411	0.83[AMR][1000 genomes]
rs17195474	0.83[AMR][1000 genomes]
rs17195488	0.83[AMR][1000 genomes]
rs17195516	0.83[AMR][1000 genomes]
rs2106069	0.83[AMR][1000 genomes]
rs2239514	0.83[AMR][1000 genomes]
rs2239515	0.83[AMR][1000 genomes]
rs2239516	0.83[AMR][1000 genomes]
rs2267638	0.83[AMR][1000 genomes]
rs2267640	0.83[AMR][1000 genomes]
rs2302347	0.83[AMR][1000 genomes]
rs2394387	0.83[AMR][1000 genomes]
rs2394388	0.83[AMR][1000 genomes]
rs2394389	0.83[AMR][1000 genomes]
rs3815101	0.83[AMR][1000 genomes]
rs4148247	0.83[AMR][1000 genomes]
rs57626358	0.83[AMR][1000 genomes]
rs59272830	0.83[AMR][1000 genomes]
rs59607822	0.83[AMR][1000 genomes]
rs59913575	0.83[AMR][1000 genomes]
rs60081418	0.83[AMR][1000 genomes]
rs60365864	0.83[AMR][1000 genomes]
rs6457246	0.83[AMR][1000 genomes]
rs6457247	0.83[AMR][1000 genomes]
rs6457248	0.83[AMR][1000 genomes]
rs6457249	0.83[AMR][1000 genomes]
rs6899769	0.83[AMR][1000 genomes]
rs6901251	0.83[AMR][1000 genomes]
rs6911174	0.83[AMR][1000 genomes]
rs6917434	0.83[AMR][1000 genomes]
rs6917935	0.83[AMR][1000 genomes]
rs6934466	0.83[AMR][1000 genomes]
rs7742291	0.83[AMR][1000 genomes]
rs7742650	0.83[AMR][1000 genomes]
rs7742754	0.83[AMR][1000 genomes]
rs7749109	0.83[AMR][1000 genomes]
rs7749807	0.83[AMR][1000 genomes]
rs7749978	0.83[AMR][1000 genomes]
rs7767002	0.83[AMR][1000 genomes]
rs9671	0.83[AMR][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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer 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	825 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3888777	ENSG00000204576	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30526000-30530200	Weak transcription	Pancreas	Pancrea
2	chr6:30526000-30530200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:30526000-30530800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:30526000-30537800	Weak transcription	Small Intestine	intestine
5	chr6:30526000-30538400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:30526000-30538600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30526200-30530200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:30526200-30530200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:30526200-30530200	Weak transcription	HSMMtube	muscle
10	chr6:30526200-30530200	Weak transcription	NHEK	skin
11	chr6:30526200-30530600	Weak transcription	Fetal Kidney	kidney
12	chr6:30526200-30538200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:30526400-30530000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:30526400-30531600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:30526400-30532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:30526400-30538000	Weak transcription	HUVEC	blood vessel
17	chr6:30526400-30538000	Weak transcription	NHDF-Ad	bronchial
18	chr6:30526600-30530200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:30526600-30530200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:30526600-30536000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:30526600-30537800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:30526800-30530000	Weak transcription	Hela-S3	cervix
23	chr6:30526800-30537600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:30526800-30538200	Weak transcription	Fetal Brain Male	brain
25	chr6:30526800-30538200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:30527600-30532200	Strong transcription	Fetal Muscle Leg	muscle
27	chr6:30527600-30532400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:30527600-30538000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:30528200-30532200	Strong transcription	Brain Germinal Matrix	brain
30	chr6:30528600-30531000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:30528600-30531400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:30528600-30531400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:30528600-30531400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:30528600-30531400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:30528600-30531400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:30528600-30531600	Strong transcription	HSMM	muscle
37	chr6:30528600-30532000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:30528600-30532200	Strong transcription	Fetal Thymus	thymus
39	chr6:30528600-30532200	Strong transcription	Dnd41	blood
40	chr6:30528800-30531400	Strong transcription	Placenta	Placenta
41	chr6:30528800-30531800	Strong transcription	Fetal Brain Female	brain
42	chr6:30528800-30532000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:30528800-30532000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:30528800-30532200	Strong transcription	Primary T cells from cord blood	blood
45	chr6:30528800-30532400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:30529000-30530200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr6:30529000-30531000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:30529000-30531000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:30529000-30531200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr6:30529000-30531200	Strong transcription	Duodenum Mucosa	Duodenum

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