Variant report

Variant	rs7775389
Chromosome Location	chr6:119466590-119466591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119453269..119456548-chr6:119464804..119468578,3	MCF-7	breast:
2	chr6:119449639..119451430-chr6:119466197..119468847,2	K562	blood:
3	chr6:119464932..119466887-chr6:119670383..119671900,2	MCF-7	breast:
4	chr6:119455611..119461723-chr6:119466568..119469851,5	K562	blood:
5	chr6:119455611..119458749-chr6:119466100..119469942,4	K562	blood:
6	chr6:119465818..119467517-chr6:119472124..119474189,2	K562	blood:

Variant related genes	Relation type
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12190611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891540	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608541	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs611211	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs624829	0.88[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs638368	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs656012	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs666655	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs678974	0.87[EUR][1000 genomes]
rs682949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs683488	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6910397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928078	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6935092	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706983	0.82[MEX][hapmap]
rs733259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733260	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398503	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7775389	MAD2L1BP	trans	cerebellum	SCAN
rs7775389	FAM184A	cis	parietal	SCAN
rs7775389	FAM162B	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119450600-119469600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:119451400-119468800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:119457000-119474800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:119459000-119469000	Weak transcription	Lung	lung
5	chr6:119459200-119468000	Weak transcription	Placenta	Placenta
6	chr6:119459400-119467800	Weak transcription	NHLF	lung
7	chr6:119460800-119467600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:119461600-119467800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:119461800-119468600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:119462600-119467800	Weak transcription	Fetal Heart	heart
11	chr6:119462600-119468000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:119462800-119467800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:119465800-119466600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:119465800-119466800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:119465800-119467200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr6:119465800-119468000	Enhancers	K562	blood
17	chr6:119465800-119468800	Enhancers	HepG2	liver
18	chr6:119465800-119468800	Enhancers	NHDF-Ad	bronchial
19	chr6:119465800-119469800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:119466000-119466600	Enhancers	Primary hematopoietic stem cells	blood
21	chr6:119466000-119466600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:119466000-119466600	Enhancers	Hela-S3	cervix
23	chr6:119466000-119466800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:119466000-119466800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:119466000-119467000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:119466000-119467800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:119466000-119469000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:119466000-119469400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:119466000-119469800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:119466200-119466600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:119466200-119466600	Enhancers	Fetal Thymus	thymus
32	chr6:119466200-119466800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr6:119466200-119466800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:119466200-119466800	Enhancers	Dnd41	blood
35	chr6:119466200-119467000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:119466200-119467800	Enhancers	Primary T cells from cord blood	blood
37	chr6:119466200-119468000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr6:119466200-119468000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:119466200-119469800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:119466200-119469800	Enhancers	HUVEC	blood vessel
41	chr6:119466200-119470200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:119466400-119466600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:119466400-119466600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:119466400-119466600	Enhancers	Fetal Lung	lung
45	chr6:119466400-119466800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr6:119466400-119466800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr6:119466400-119467200	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr6:119466400-119467600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:119466400-119467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:119466400-119467800	Weak transcription	Stomach Mucosa	stomach

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