Variant report

Variant	rs1874229
Chromosome Location	chr6:74228006-74228007
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74221323..74236726-chr6:74306065..74338770,101	K562	blood:
2	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
3	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
4	chr6:74225345..74228338-chr6:74268407..74270549,2	K562	blood:
5	chr6:74160323..74161865-chr6:74226774..74228460,2	MCF-7	breast:
6	chr6:74169658..74172596-chr6:74225769..74229058,3	MCF-7	breast:
7	chr6:74225495..74228323-chr6:74275867..74278333,2	MCF-7	breast:
8	chr6:74225719..74228474-chr6:74264854..74267464,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000119899	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000218459	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1128073	0.85[EUR][1000 genomes]
rs1245347	0.92[EUR][1000 genomes]
rs13203367	0.91[EUR][1000 genomes]
rs1390081	0.95[EUR][1000 genomes]
rs1390082	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1874230	0.81[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2017272	0.85[EUR][1000 genomes]
rs2073466	0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2291719	0.94[EUR][1000 genomes]
rs2882584	0.84[EUR][1000 genomes]
rs3822960	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4257823	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4708062	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs473805	0.84[ASN][1000 genomes]
rs514582	0.80[EUR][1000 genomes]
rs569652	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs577372	0.83[TSI][hapmap]
rs613787	0.82[EUR][1000 genomes]
rs617464	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs642722	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6453679	0.92[EUR][1000 genomes]
rs673265	0.84[EUR][1000 genomes]
rs6915328	0.95[EUR][1000 genomes]
rs6918753	0.92[EUR][1000 genomes]
rs693434	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7741376	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7751342	0.81[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs7767833	0.87[EUR][1000 genomes]
rs7771730	0.90[EUR][1000 genomes]
rs9352001	0.85[EUR][1000 genomes]
rs9352003	0.81[EUR][1000 genomes]
rs9352005	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs9442916	0.92[EUR][1000 genomes]
rs9446917	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
9	nsv5350	chr6:74221995-74267088	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
10	nsv886159	chr6:74223153-74275405	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
11	nsv981157	chr6:74227071-74229370	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1874229	EEF1A1	cis	parietal	SCAN
rs1874229	EEF1A1	Cis_1M	lymphoblastoid	RTeQTL
rs1874229	C6orf221	cis	cerebellum	SCAN
rs1874229	EEF1A1	cis	cerebellum	SCAN
rs1874229	MTO1	Cis_1M	lymphoblastoid	RTeQTL
rs1874229	SMAP1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74172200-74229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:74187600-74228400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:74224200-74228600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:74224200-74229000	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr6:74224200-74229000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:74224200-74229200	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr6:74224400-74228400	Genic enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:74224400-74228400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr6:74224600-74228400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:74224600-74228400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:74224600-74229000	Genic enhancers	Primary B cells from cord blood	blood
12	chr6:74224600-74229000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:74224600-74230600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
14	chr6:74224800-74228400	Genic enhancers	Stomach Smooth Muscle	stomach
15	chr6:74224800-74229000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:74224800-74230600	Transcr. at gene 5' and 3'	A549	lung
17	chr6:74225000-74228200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:74225000-74228400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:74225000-74228400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:74225000-74228400	Genic enhancers	Brain Anterior Caudate	brain
21	chr6:74225000-74228400	Genic enhancers	Brain Substantia Nigra	brain
22	chr6:74225000-74228400	Strong transcription	Esophagus	oesophagus
23	chr6:74225000-74228400	Genic enhancers	Rectal Smooth Muscle	rectum
24	chr6:74225000-74229000	Genic enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:74225000-74230000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:74225000-74230000	Transcr. at gene 5' and 3'	NH-A	brain
27	chr6:74225000-74231600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:74225200-74228400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:74225200-74228400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:74225400-74228400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:74225400-74228400	Strong transcription	Brain Germinal Matrix	brain
32	chr6:74225600-74230000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:74225600-74230000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:74225600-74230000	Transcr. at gene 5' and 3'	K562	blood
35	chr6:74225600-74230600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:74225800-74230000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
37	chr6:74225800-74230000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
38	chr6:74225800-74230000	Transcr. at gene 5' and 3'	Osteobl	bone
39	chr6:74225800-74230600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:74226000-74228400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:74226000-74229000	Genic enhancers	Small Intestine	intestine
42	chr6:74226000-74230400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
43	chr6:74226000-74230600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:74226000-74230600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
45	chr6:74226000-74230800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
46	chr6:74226200-74228400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
47	chr6:74226200-74230600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:74226400-74228400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr6:74226400-74230200	Transcr. at gene 5' and 3'	Hela-S3	cervix
50	chr6:74226400-74230600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell

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