Variant report

Variant	rs9296177
Chromosome Location	chr6:36197742-36197743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36197473..36201829-chr6:36205316..36210325,5	MCF-7	breast:
2	chr6:36192518..36194970-chr6:36195134..36199555,3	K562	blood:
3	chr6:36161641..36166728-chr6:36193210..36198515,8	K562	blood:
4	chr6:36194084..36196042-chr6:36196761..36199323,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096070	Chromatin interaction
ENSG00000246982	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10807157	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10947591	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196677	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12197499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13196184	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17356524	1.00[JPT][hapmap]
rs2032506	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234075	1.00[CHB][hapmap]
rs2301422	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34262487	1.00[ASN][1000 genomes]
rs4236048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6457892	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906612	0.93[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs71569325	1.00[ASN][1000 genomes]
rs7747793	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773924	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366900	0.82[EUR][1000 genomes]
rs9470228	0.93[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9296177	C6orf106	cis	cerebellum	SCAN
rs9296177	RP1-179N16.6	cis	Nerve Tibial	GTEx
rs9296177	BAK1	cis	cerebellum	SCAN
rs9296177	PNPLA1	cis	parietal	SCAN
rs9296177	RP1-179N16.6	cis	Thyroid	GTEx
rs9296177	MAPK13	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36164400-36203000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36166600-36200200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:36166800-36201800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:36167000-36201800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:36167200-36201400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:36167400-36201600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:36167600-36199800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:36167600-36201200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:36167800-36201400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr6:36168000-36200400	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr6:36168000-36201400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:36169400-36201800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:36170000-36201800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:36172200-36202000	Strong transcription	Thymus	Thymus
15	chr6:36172600-36201400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr6:36172600-36201600	Strong transcription	Liver	Liver
17	chr6:36172600-36202000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:36173000-36201200	Strong transcription	Dnd41	blood
19	chr6:36173400-36202600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:36174000-36204600	Strong transcription	Primary T cells from cord blood	blood
21	chr6:36174200-36201800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr6:36174400-36201600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:36179400-36197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:36183600-36199200	Genic enhancers	Fetal Intestine Small	intestine
25	chr6:36185800-36210600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:36186200-36202600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:36189000-36202600	Strong transcription	Fetal Muscle Leg	muscle
28	chr6:36189000-36204800	Strong transcription	Fetal Stomach	stomach
29	chr6:36189200-36201400	Strong transcription	Osteobl	bone
30	chr6:36189200-36202400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:36189400-36200200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:36189400-36201400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:36189400-36201400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:36189600-36200000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:36189600-36200200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:36189600-36201200	Strong transcription	Fetal Lung	lung
37	chr6:36189600-36201400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:36189600-36201800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:36189600-36201800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:36189600-36204400	Strong transcription	Brain Germinal Matrix	brain
41	chr6:36189800-36199800	Strong transcription	Aorta	Aorta
42	chr6:36189800-36202800	Strong transcription	Brain Hippocampus Middle	brain
43	chr6:36189800-36203800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr6:36192000-36200200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:36192200-36198400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr6:36192200-36203400	Weak transcription	Right Atrium	heart
47	chr6:36192400-36201200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:36192400-36202200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:36193000-36198200	Strong transcription	HSMM	muscle
50	chr6:36193000-36199200	Strong transcription	Primary monocytes fromperipheralblood	blood

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