Variant report

Variant	rs2394249
Chromosome Location	chr6:29940786-29940787
allele	A/T
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	chr6:29936914-29943239	K562	blood:	n/a	n/a

Variant related genes	Relation type
HCG9	TF binding region
MICD	TF binding region

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10484549	0.95[EUR][1000 genomes]
rs1056243	1.00[AFR][1000 genomes]
rs16896044	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16896851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16896923	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16896970	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17179992	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17180093	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17180107	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17180227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17180836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17187693	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17193696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991955	1.00[AFR][1000 genomes]
rs1991956	1.00[AFR][1000 genomes]
rs2074485	1.00[AFR][1000 genomes]
rs2240073	1.00[AFR][1000 genomes]
rs2286404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2893999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869062	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4087724	1.00[AFR][1000 genomes]
rs4087726	1.00[AFR][1000 genomes]
rs41540614	1.00[AFR][1000 genomes]
rs41545022	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs41545117	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs41547618	1.00[AFR][1000 genomes]
rs41562213	1.00[AFR][1000 genomes]
rs4599690	1.00[AFR][1000 genomes]
rs55664658	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55676227	1.00[AFR][1000 genomes]
rs55748016	1.00[AFR][1000 genomes]
rs55795233	1.00[AFR][1000 genomes]
rs55803658	1.00[AFR][1000 genomes]
rs55808509	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55897388	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55901207	1.00[AFR][1000 genomes]
rs55975201	1.00[AFR][1000 genomes]
rs56052321	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56073777	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56079109	1.00[AFR][1000 genomes]
rs56147022	1.00[AFR][1000 genomes]
rs56149225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56171155	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56181708	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56185319	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56232426	1.00[AFR][1000 genomes]
rs56262516	0.83[ASN][1000 genomes]
rs56263834	1.00[AFR][1000 genomes]
rs56270681	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56285764	1.00[AFR][1000 genomes]
rs56289102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369124	1.00[AFR][1000 genomes]
rs56378970	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs58161072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58309428	1.00[AFR][1000 genomes]
rs61180635	1.00[AFR][1000 genomes]
rs62388660	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62388661	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62388723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388749	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62388750	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388751	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388752	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388754	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388755	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388756	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388757	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388764	1.00[AFR][1000 genomes]
rs62388798	1.00[AFR][1000 genomes]
rs62388799	1.00[AFR][1000 genomes]
rs62388801	1.00[AFR][1000 genomes]
rs62388802	1.00[AFR][1000 genomes]
rs62389590	1.00[AFR][1000 genomes]
rs62389592	1.00[AFR][1000 genomes]
rs62390160	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62390162	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62390181	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62390374	1.00[AFR][1000 genomes]
rs62390375	1.00[AFR][1000 genomes]
rs62390376	1.00[AFR][1000 genomes]
rs62390377	1.00[AFR][1000 genomes]
rs62390378	1.00[AFR][1000 genomes]
rs62390379	1.00[AFR][1000 genomes]
rs62390400	1.00[AFR][1000 genomes]
rs62390401	1.00[AFR][1000 genomes]
rs62390402	1.00[AFR][1000 genomes]
rs62390510	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62390517	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62390553	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62390555	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62392214	1.00[AFR][1000 genomes]
rs62392216	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6939037	0.93[ASN][1000 genomes]
rs9260794	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	esv32544	chr6:29831716-29944103	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active 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 target site	28 gene(s)	inside rSNPs	diseases
15	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers 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 target site	28 gene(s)	inside rSNPs	diseases
16	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
18	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
20	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	nsv984584	chr6:29932342-29943951	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
24	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
25	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29933600-29942400	Weak transcription	Lung	lung
2	chr6:29934400-29944200	Weak transcription	Aorta	Aorta
3	chr6:29934800-29942600	Weak transcription	Brain Substantia Nigra	brain
4	chr6:29935400-29942600	Weak transcription	GM12878-XiMat	blood
5	chr6:29935400-29943400	Weak transcription	Small Intestine	intestine
6	chr6:29935600-29942600	Weak transcription	Brain Anterior Caudate	brain
7	chr6:29935600-29944800	Weak transcription	Dnd41	blood
8	chr6:29935800-29942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:29936000-29942800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:29936200-29942000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:29936200-29942400	Weak transcription	Right Atrium	heart
12	chr6:29936200-29942400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:29936400-29941400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:29936400-29942600	Weak transcription	HepG2	liver
15	chr6:29936400-29943000	Weak transcription	Psoas Muscle	Psoas
16	chr6:29936600-29942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:29936600-29942400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:29936600-29942800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:29936600-29942800	Weak transcription	HSMMtube	muscle
20	chr6:29936800-29942800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:29937200-29942800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:29937800-29942800	Weak transcription	K562	blood
23	chr6:29938600-29942800	Weak transcription	Colonic Mucosa	Colon
24	chr6:29939000-29941600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:29939200-29940800	Strong transcription	Fetal Intestine Small	intestine
26	chr6:29939200-29942600	Weak transcription	Adipose Nuclei	Adipose
27	chr6:29939600-29941000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr6:29939800-29940800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:29939800-29940800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr6:29940000-29940800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr6:29940000-29940800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr6:29940000-29940800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:29940200-29940800	Genic enhancers	Gastric	stomach
34	chr6:29940400-29940800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
35	chr6:29940400-29940800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:29940600-29942000	Weak transcription	Pancreas	Pancrea
37	chr6:29940600-29942200	Weak transcription	Right Ventricle	heart
38	chr6:29940600-29942400	Weak transcription	Left Ventricle	heart
39	chr6:29940600-29942400	Weak transcription	Spleen	Spleen
40	chr6:29940600-29942600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links