Variant report

Variant	rs9295930
Chromosome Location	chr6:30849822-30849823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30849612-30852127	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr6:30849649-30849991	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:30849757-30850062	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr6:30849706-30849918	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:30848256-30850089	H1-neurons	neurons:	n/a	n/a
6	ELF1	chr6:30849626-30850154	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:30849670-30850114	U87	brain:	n/a	n/a
8	MAZ	chr6:30849357-30850904	IMR90	lung:	n/a	n/a
9	POLR2A	chr6:30848255-30854769	H1-neurons	neurons:	n/a	n/a
10	SIN3A	chr6:30848439-30851375	H1-hESC	embryonic stem cell:	n/a	chr6:30850626-30850634 chr6:30848762-30848775 chr6:30848769-30848782 chr6:30849877-30849886 chr6:30850627-30850636
11	REST	chr6:30848004-30855226	H1-neurons	neurons:	n/a	chr6:30850005-30850018 chr6:30849842-30849855 chr6:30848363-30848383 chr6:30848363-30848383 chr6:30848771-30848781 chr6:30850231-30850245 chr6:30849152-30849172 chr6:30848363-30848383 chr6:30854903-30854911 chr6:30848769-30848782 chr6:30848762-30848775 chr6:30848256-30848264
12	ZNF143	chr6:30849746-30850570	H1-hESC	embryonic stem cell:	n/a	chr6:30849873-30849891 chr6:30850154-30850172

No.	Distal block	Cell Line	Cell type
1	chr6:30847750..30851239-chr6:30880214..30883075,5	K562	blood:
2	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
3	chr6:30847234..30851507-chr6:30857768..30862295,8	K562	blood:
4	chr6:30849765..30853673-chr6:30873635..30876591,7	MCF-7	breast:
5	chr6:30670303..30672566-chr6:30849321..30851988,2	MCF-7	breast:
6	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
7	chr6:30814424..30817937-chr6:30849019..30852528,4	MCF-7	breast:
8	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
9	chr6:30848838..30854096-chr6:30874501..30878794,8	MCF-7	breast:
10	chr6:30849687..30852078-chr6:30875212..30877587,2	K562	blood:
11	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
12	chr6:30688723..30690650-chr6:30849267..30850908,2	K562	blood:
13	chr6:30849184..30852666-chr6:30852715..30854490,5	K562	blood:
14	chr6:30685105..30690458-chr6:30847596..30854595,13	MCF-7	breast:

Variant related genes	Relation type
DDR1	TF binding region
ENSG00000196230	Chromatin interaction
ENSG00000264731	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000237923	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000224328	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10947113	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947114	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528271	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12697941	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074511	0.89[EUR][1000 genomes]
rs2239518	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2240803	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267641	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285319	0.83[EUR][1000 genomes]
rs2286655	0.89[EUR][1000 genomes]
rs2286656	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2524236	0.82[EUR][1000 genomes]
rs3213644	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3916232	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711247	0.83[EUR][1000 genomes]
rs4711249	0.89[EUR][1000 genomes]
rs4713402	0.89[EUR][1000 genomes]
rs9295928	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295933	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9366761	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9368646	0.89[EUR][1000 genomes]
rs9394021	0.83[EUR][1000 genomes]
rs9461639	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468841	0.86[AMR][1000 genomes]
rs9468843	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468847	0.89[EUR][1000 genomes]
rs9501030	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9501035	0.89[EUR][1000 genomes]
rs9501340	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9501491	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv884110	chr6:30845563-30856463	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv884111	chr6:30845563-30864279	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
9	nsv884112	chr6:30845563-30866618	Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	nsv601482	chr6:30846830-30854090	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884113	chr6:30846830-30857542	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv884114	chr6:30846830-30867830	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv884115	chr6:30847710-30858991	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
14	nsv884116	chr6:30848253-30864279	Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
15	nsv884117	chr6:30849124-30862423	Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
16	nsv884118	chr6:30849822-30855907	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
17	nsv884119	chr6:30849822-30856692	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
18	nsv884120	chr6:30849822-30864279	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9295930	HIST1H2AM	cis	cerebellum	SCAN
rs9295930	VARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30844200-30850200	Weak transcription	Spleen	Spleen
2	chr6:30845800-30850000	Weak transcription	Primary B cells from cord blood	blood
3	chr6:30845800-30850800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:30845800-30851200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:30846000-30850000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:30846000-30850000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:30846000-30850000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:30846000-30850200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:30846000-30850200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:30846000-30850400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:30846000-30850400	Weak transcription	Left Ventricle	heart
12	chr6:30846000-30850400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:30846000-30850600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:30846000-30850800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:30846000-30850800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:30846000-30850800	Weak transcription	Dnd41	blood
17	chr6:30846000-30850800	Enhancers	K562	blood
18	chr6:30846000-30851200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:30846000-30851400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:30846000-30851600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:30846000-30851600	Weak transcription	Liver	Liver
22	chr6:30846000-30851600	Weak transcription	HUVEC	blood vessel
23	chr6:30846200-30850200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:30846200-30850400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:30846200-30850800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:30846200-30851200	Weak transcription	Psoas Muscle	Psoas
27	chr6:30846200-30851400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:30846400-30850800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:30846600-30850000	Weak transcription	Adipose Nuclei	Adipose
30	chr6:30846800-30850400	Weak transcription	Hela-S3	cervix
31	chr6:30848200-30851400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:30848200-30851600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr6:30848400-30850200	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr6:30848400-30850200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr6:30848400-30850800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:30848400-30851600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:30848600-30850200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:30848600-30850400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:30848600-30850400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr6:30848600-30851000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:30848600-30852000	Enhancers	NH-A	brain
42	chr6:30848800-30850400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:30848800-30850400	Flanking Active TSS	HSMMtube	muscle
44	chr6:30848800-30850600	Enhancers	Fetal Intestine Large	intestine
45	chr6:30848800-30850800	Enhancers	Placenta	Placenta
46	chr6:30848800-30851600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr6:30848800-30851600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:30848800-30851800	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr6:30849000-30850000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr6:30849000-30850200	Flanking Active TSS	Fetal Kidney	kidney

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