Variant report

Variant	rs9262141
Chromosome Location	chr6:30644137-30644138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30642917-30644147	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr6:30643576-30644234	GM12892	blood:	n/a	n/a
3	PML	chr6:30643626-30644313	K562	blood:	n/a	n/a
4	POLR2A	chr6:30643532-30644606	K562	blood:	n/a	n/a
5	POLR2A	chr6:30643573-30644447	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:30643836-30644188	HL-60	blood:	n/a	n/a
7	POLR2A	chr6:30643446-30644161	HUVEC	blood vessel:	n/a	n/a
8	PML	chr6:30643447-30644199	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:30643367-30645364	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr6:30643778-30644886	K562	blood:	n/a	n/a
11	POLR2A	chr6:30643842-30644209	K562	blood:	n/a	n/a
12	POLR2A	chr6:30643440-30645279	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:30643620-30644176	GM12892	blood:	n/a	n/a
14	POLR2A	chr6:30643858-30644182	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30643140..30646430-chr6:30646778..30649546,3	MCF-7	breast:
2	chr6:30642982..30645092-chr6:30648552..30650727,2	MCF-7	breast:
3	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
4	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
5	chr6:30639491..30642399-chr6:30642819..30647161,4	MCF-7	breast:
6	chr6:30642470..30648471-chr6:30697241..30700740,8	MCF-7	breast:
7	chr6:30581230..30587315-chr6:30638443..30644329,12	MCF-7	breast:
8	chr6:30577127..30589352-chr6:30620628..30648657,88	K562	blood:
9	chr6:30643814..30650234-chr6:30705979..30710789,12	MCF-7	breast:
10	chr6:30582956..30585804-chr6:30643199..30647453,3	MCF-7	breast:

No data

Variant related genes	Relation type
DHX16	TF binding region
ENSG00000137312	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1059612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1264347	0.90[AMR][1000 genomes]
rs1264351	1.00[AMR][1000 genomes]
rs1264373	1.00[AMR][1000 genomes]
rs2263298	0.90[AMR][1000 genomes]
rs2517578	0.90[AMR][1000 genomes]
rs2524266	0.83[AMR][1000 genomes]
rs2535332	0.90[AMR][1000 genomes]
rs2535334	0.90[AMR][1000 genomes]
rs3094023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3094118	0.80[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3095327	0.85[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130665	0.80[EUR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes]
rs3130670	0.83[AMR][1000 genomes]
rs3131112	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3132582	0.85[EUR][1000 genomes]
rs3132583	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132600	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262143	1.00[EUR][1000 genomes]
rs9262146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	406 gene(s)	inside rSNPs	diseases
7	nsv884094	chr6:30637998-30660611	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv823472	chr6:30638581-30644218	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9262141	HIST1H2BM	cis	cerebellum	SCAN
rs9262141	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30640800-30644400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:30640800-30644400	Weak transcription	Aorta	Aorta
3	chr6:30640800-30644400	Weak transcription	Gastric	stomach
4	chr6:30640800-30647000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:30640800-30649600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:30641000-30644200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:30641000-30644400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:30641000-30644400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:30641000-30644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:30641000-30647000	Weak transcription	Stomach Mucosa	stomach
11	chr6:30641000-30647600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:30641000-30650000	Weak transcription	Psoas Muscle	Psoas
13	chr6:30641200-30644200	Enhancers	Liver	Liver
14	chr6:30641200-30644200	Weak transcription	Brain Anterior Caudate	brain
15	chr6:30641200-30644200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:30641200-30644400	Weak transcription	Brain Angular Gyrus	brain
17	chr6:30641200-30644400	Weak transcription	Brain Substantia Nigra	brain
18	chr6:30641200-30644600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:30641200-30645000	Weak transcription	Fetal Kidney	kidney
20	chr6:30641200-30646800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:30641200-30647000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:30641400-30644200	Weak transcription	Primary B cells from cord blood	blood
23	chr6:30641400-30646600	Weak transcription	Fetal Brain Male	brain
24	chr6:30641800-30646800	Weak transcription	HepG2	liver
25	chr6:30643600-30644600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr6:30643600-30644600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr6:30643600-30644800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:30643600-30645000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:30643600-30645200	Strong transcription	Primary hematopoietic stem cells	blood
30	chr6:30643600-30645200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:30643600-30645400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:30643600-30645600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:30643600-30645800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr6:30643600-30646000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:30643600-30646000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:30643600-30646000	Strong transcription	HUVEC	blood vessel
37	chr6:30643600-30646200	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr6:30643600-30646400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr6:30643600-30646400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:30643600-30646400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:30643600-30646600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:30643600-30646600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:30643600-30646600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr6:30643600-30646600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:30643600-30646600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:30643600-30646600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:30643600-30646600	Strong transcription	Fetal Thymus	thymus
48	chr6:30643600-30646600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:30643600-30646600	Strong transcription	HSMM	muscle
50	chr6:30643600-30646600	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links