Variant report

Variant	rs2844715
Chromosome Location	chr6:30516353-30516354
allele	C/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	CEBPB	chr6:30516141-30516423	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:30515814-30517937	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:30515933-30517660	K562	blood:	n/a	n/a
4	POLR2A	chr6:30516163-30516403	K562	blood:	n/a	n/a
5	POLR2A	chr6:30515978-30516618	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:30515940-30516376	GM12892	blood:	n/a	n/a
7	POLR2A	chr6:30515930-30516658	GM12891	blood:	n/a	n/a
8	POLR2A	chr6:30515956-30516442	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:30516013-30516520	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:30515919-30516487	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30515029..30517945-chr6:30687848..30689600,2	MCF-7	breast:
2	chr6:30456233..30458603-chr6:30513714..30516752,3	MCF-7	breast:
3	chr6:30450929..30459545-chr6:30516289..30528141,20	K562	blood:

Variant related genes	Relation type
GNL1	TF binding region
ENSG00000196230	Chromatin interaction
ENSG00000236603	Chromatin interaction
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1058318	0.88[EUR][1000 genomes]
rs1264432	0.81[EUR][1000 genomes]
rs1264437	0.83[EUR][1000 genomes]
rs1264438	0.84[EUR][1000 genomes]
rs1264439	0.83[EUR][1000 genomes]
rs1264440	0.92[EUR][1000 genomes]
rs1264448	0.83[EUR][1000 genomes]
rs1362119	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1468079	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2023608	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2023609	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074503	0.88[EUR][1000 genomes]
rs2074504	0.85[EUR][1000 genomes]
rs2074505	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109477	0.81[AMR][1000 genomes]
rs2269709	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2269710	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2429655	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429656	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2508021	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508022	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2508023	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2508024	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2516639	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2516641	0.88[EUR][1000 genomes]
rs2516642	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2516643	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2516644	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516646	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2516647	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516648	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2516649	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2516653	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516655	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2516656	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2516659	0.84[AMR][1000 genomes]
rs2516662	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2524221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524223	0.87[EUR][1000 genomes]
rs2524224	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2524225	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2524226	0.87[EUR][1000 genomes]
rs2534802	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2534803	0.81[EUR][1000 genomes]
rs2534804	0.81[EUR][1000 genomes]
rs2534805	0.82[EUR][1000 genomes]
rs2534806	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2534807	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2534808	0.84[EUR][1000 genomes]
rs2534809	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2534810	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2534811	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2534812	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2534813	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2534814	0.84[EUR][1000 genomes]
rs2534815	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2534817	0.81[EUR][1000 genomes]
rs2534821	0.85[EUR][1000 genomes]
rs2534823	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2534824	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2534825	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844716	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844717	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844718	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844720	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844721	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2844722	0.81[AMR][1000 genomes]
rs2844723	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844724	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844725	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3094718	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095280	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3130039	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3130041	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130043	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130045	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130240	0.91[EUR][1000 genomes]
rs3130242	0.87[EUR][1000 genomes]
rs3130243	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130244	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3132609	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132612	0.84[EUR][1000 genomes]
rs3132613	0.87[EUR][1000 genomes]
rs3132614	0.89[EUR][1000 genomes]
rs9262070	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9262082	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9262118	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs975195	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs996588	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs996589	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer 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	825 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30509800-30519600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:30509800-30523000	Weak transcription	A549	lung
3	chr6:30510000-30521200	Weak transcription	Hela-S3	cervix
4	chr6:30510000-30522400	Weak transcription	Fetal Heart	heart
5	chr6:30510000-30523000	Weak transcription	Right Atrium	heart
6	chr6:30510200-30519000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:30510800-30520000	Weak transcription	Fetal Brain Male	brain
8	chr6:30511600-30522600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr6:30511800-30522600	Strong transcription	Placenta	Placenta
10	chr6:30512400-30522000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:30512400-30522200	Strong transcription	Fetal Stomach	stomach
12	chr6:30512600-30517400	Weak transcription	NH-A	brain
13	chr6:30512600-30522400	Strong transcription	Fetal Thymus	thymus
14	chr6:30512800-30522000	Strong transcription	Fetal Intestine Small	intestine
15	chr6:30512800-30522000	Strong transcription	Lung	lung
16	chr6:30512800-30522000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr6:30512800-30522200	Strong transcription	HepG2	liver
18	chr6:30512800-30522400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:30512800-30522400	Strong transcription	Primary B cells from cord blood	blood
20	chr6:30512800-30522400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:30513000-30518800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:30513000-30520600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:30513000-30522000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:30513000-30522000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:30513000-30522200	Strong transcription	Fetal Intestine Large	intestine
26	chr6:30513200-30517400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr6:30513200-30522000	Strong transcription	Liver	Liver
28	chr6:30513200-30522000	Strong transcription	Brain Hippocampus Middle	brain
29	chr6:30513200-30522200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:30513200-30522200	Strong transcription	Brain Anterior Caudate	brain
31	chr6:30513200-30522200	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:30513200-30522400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:30513200-30522400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:30513200-30522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:30513200-30522400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:30513200-30522400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:30513200-30522400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:30513200-30522600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:30513200-30522600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:30513200-30522600	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr6:30513200-30522600	Strong transcription	Dnd41	blood
42	chr6:30513200-30523000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:30513400-30516600	Strong transcription	Aorta	Aorta
44	chr6:30513400-30517200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:30513400-30517600	Strong transcription	Left Ventricle	heart
46	chr6:30513400-30519200	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr6:30513400-30520200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:30513400-30521800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:30513400-30522000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:30513400-30522000	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links