Variant report

Variant	rs6910397
Chromosome Location	chr6:119468879-119468880
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119450270..119451239-chr6:119468206..119470213,5	MCF-7	breast:
2	chr6:119256106..119257947-chr6:119468580..119471034,2	K562	blood:
3	chr6:119467858..119470789-chr6:119668770..119672252,3	K562	blood:
4	chr6:119455611..119461723-chr6:119466568..119469851,5	K562	blood:
5	chr6:119467902..119470326-chr6:119670828..119672747,2	MCF-7	breast:
6	chr6:119455611..119458749-chr6:119466100..119469942,4	K562	blood:

Variant related genes	Relation type
ENSG00000111885	Chromatin interaction
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12190611	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891540	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608541	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs611211	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs624829	0.89[ASW][hapmap];0.87[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs638368	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[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	0.83[AMR][1000 genomes];0.97[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];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs683488	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928078	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6935092	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775389	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]
rs9387637	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398502	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398503	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[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
rs6910397	FAM162B	cis	cerebellum	SCAN
rs6910397	FAM184A	cis	parietal	SCAN
rs6910397	MAD2L1BP	trans	cerebellum	SCAN

Chromatin state (count:82 , 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	chr6:119457000-119474800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:119459000-119469000	Weak transcription	Lung	lung
4	chr6:119465800-119469800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:119466000-119469000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:119466000-119469400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:119466000-119469800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:119466200-119469800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:119466200-119469800	Enhancers	HUVEC	blood vessel
10	chr6:119466200-119470200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:119466600-119469400	Weak transcription	Fetal Lung	lung
12	chr6:119466800-119469000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:119466800-119470200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:119467600-119469200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:119467600-119469400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:119467600-119469800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:119467600-119470200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:119467600-119470200	Enhancers	Hela-S3	cervix
19	chr6:119467800-119469600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:119467800-119469800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:119467800-119469800	Enhancers	Fetal Heart	heart
22	chr6:119467800-119469800	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:119467800-119469800	Enhancers	HSMM	muscle
24	chr6:119467800-119470200	Enhancers	Stomach Mucosa	stomach
25	chr6:119467800-119470600	Enhancers	NHLF	lung
26	chr6:119467800-119470800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:119467800-119470800	Enhancers	HMEC	breast
28	chr6:119468000-119469200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr6:119468000-119469400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:119468000-119469600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:119468000-119469800	Enhancers	Placenta	Placenta
32	chr6:119468000-119470200	Enhancers	Left Ventricle	heart
33	chr6:119468000-119470200	Enhancers	HSMMtube	muscle
34	chr6:119468200-119469200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:119468200-119469200	Flanking Active TSS	NHEK	skin
36	chr6:119468200-119469600	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:119468200-119469800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:119468200-119469800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:119468200-119469800	Enhancers	Ovary	ovary
40	chr6:119468200-119470200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:119468400-119469600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:119468400-119469800	Enhancers	Right Atrium	heart
43	chr6:119468400-119470000	Enhancers	Small Intestine	intestine
44	chr6:119468600-119469000	Flanking Active TSS	A549	lung
45	chr6:119468600-119469000	Flanking Active TSS	K562	blood
46	chr6:119468600-119469200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:119468600-119469200	Enhancers	Dnd41	blood
48	chr6:119468600-119469200	Flanking Active TSS	GM12878-XiMat	blood
49	chr6:119468600-119469400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr6:119468600-119469800	Enhancers	Fetal Muscle Leg	muscle

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