Variant report

Variant	rs2787553
Chromosome Location	chr6:106764331-106764332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106763386..106767673-chr6:106771561..106774998,5	K562	blood:
2	chr6:106763853..106765922-chr6:106766260..106768887,2	MCF-7	breast:
3	chr6:106761253..106763189-chr6:106763924..106766498,3	MCF-7	breast:
4	chr6:106754483..106756426-chr6:106762936..106765537,2	K562	blood:
5	chr6:106764300..106766114-chr6:106776359..106779349,2	K562	blood:
6	chr6:106764143..106767023-chr6:106770554..106773582,4	MCF-7	breast:
7	chr6:106762509..106764610-chr6:106766451..106770169,4	K562	blood:

Variant related genes	Relation type
ENSG00000057663	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10484575	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754416	0.96[ASN][1000 genomes]
rs11756379	0.96[ASN][1000 genomes]
rs11756420	0.96[ASN][1000 genomes]
rs11759048	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760170	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961415	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1623780	0.96[ASN][1000 genomes]
rs1624009	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624701	0.96[ASN][1000 genomes]
rs1626224	0.96[ASN][1000 genomes]
rs1626503	0.96[ASN][1000 genomes]
rs1627312	0.85[ASN][1000 genomes]
rs17488854	0.96[ASN][1000 genomes]
rs17513225	0.96[ASN][1000 genomes]
rs1766192	0.96[ASN][1000 genomes]
rs1766196	0.96[ASN][1000 genomes]
rs1766199	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1766200	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1766205	0.88[ASN][1000 genomes]
rs1769962	0.96[ASN][1000 genomes]
rs1769963	0.96[ASN][1000 genomes]
rs1769964	0.96[ASN][1000 genomes]
rs1769968	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769970	0.96[ASN][1000 genomes]
rs1769971	0.96[ASN][1000 genomes]
rs1769972	0.96[ASN][1000 genomes]
rs1769974	0.96[ASN][1000 genomes]
rs1769975	0.96[ASN][1000 genomes]
rs1769978	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1769981	0.96[ASN][1000 genomes]
rs1832408	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2743560	0.96[ASN][1000 genomes]
rs2743562	0.96[ASN][1000 genomes]
rs2743563	0.96[ASN][1000 genomes]
rs2743564	0.96[ASN][1000 genomes]
rs2757132	0.96[ASN][1000 genomes]
rs2757133	0.96[ASN][1000 genomes]
rs2763210	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763211	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763214	0.96[ASN][1000 genomes]
rs2763215	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763217	0.96[ASN][1000 genomes]
rs2763218	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763221	0.96[ASN][1000 genomes]
rs2787521	0.96[ASN][1000 genomes]
rs2787525	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787527	0.96[ASN][1000 genomes]
rs2787528	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787529	0.88[ASN][1000 genomes]
rs2787530	0.96[ASN][1000 genomes]
rs2787531	0.96[ASN][1000 genomes]
rs2787535	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787536	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787538	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787539	0.96[ASN][1000 genomes]
rs2787540	0.96[ASN][1000 genomes]
rs2787543	0.96[ASN][1000 genomes]
rs2787544	0.96[ASN][1000 genomes]
rs2787545	0.96[ASN][1000 genomes]
rs2787546	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787547	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787548	0.96[ASN][1000 genomes]
rs2787549	0.96[ASN][1000 genomes]
rs2787551	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787552	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2791114	0.96[ASN][1000 genomes]
rs2791116	0.96[ASN][1000 genomes]
rs2853338	0.96[ASN][1000 genomes]
rs2853340	0.96[ASN][1000 genomes]
rs3827647	0.96[ASN][1000 genomes]
rs41292420	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310087	0.96[ASN][1000 genomes]
rs4607457	0.89[ASN][1000 genomes]
rs543465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577707	0.96[ASN][1000 genomes]
rs595875	0.96[ASN][1000 genomes]
rs626664	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676099	0.96[ASN][1000 genomes]
rs687709	0.96[ASN][1000 genomes]
rs6920944	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930834	0.96[ASN][1000 genomes]
rs73520690	0.96[ASN][1000 genomes]
rs73522606	0.96[ASN][1000 genomes]
rs73522607	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73522610	0.96[ASN][1000 genomes]
rs73522612	0.92[ASN][1000 genomes]
rs73522614	0.96[ASN][1000 genomes]
rs73522619	0.96[ASN][1000 genomes]
rs73522625	0.96[ASN][1000 genomes]
rs73522642	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73522648	0.96[ASN][1000 genomes]
rs796707	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960323	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1035110	chr6:106557281-106802212	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv538400	chr6:106557281-106802212	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1022855	chr6:106570926-106802072	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv538401	chr6:106570926-106802072	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv1025963	chr6:106593639-106848778	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
11	nsv1020047	chr6:106597828-106912047	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv970664	chr6:106635267-106887670	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv1030367	chr6:106667748-106802072	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv538403	chr6:106667748-106802072	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106699200-106767400	Weak transcription	Stomach Mucosa	stomach
2	chr6:106718000-106771600	Weak transcription	Fetal Brain Female	brain
3	chr6:106723000-106771800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:106734800-106771800	Weak transcription	Esophagus	oesophagus
5	chr6:106735200-106773000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:106740000-106771400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:106740000-106773000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:106740200-106771400	Weak transcription	Small Intestine	intestine
9	chr6:106741000-106772200	Weak transcription	Fetal Lung	lung
10	chr6:106741200-106771400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:106751800-106771400	Weak transcription	Brain Germinal Matrix	brain
12	chr6:106757800-106771600	Weak transcription	Spleen	Spleen
13	chr6:106758200-106771400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:106758200-106772000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:106758800-106764400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:106758800-106771400	Weak transcription	Brain Anterior Caudate	brain
17	chr6:106759400-106771600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:106759400-106771600	Weak transcription	Brain Substantia Nigra	brain
19	chr6:106759600-106772000	Weak transcription	NHLF	lung
20	chr6:106760800-106771400	Weak transcription	Fetal Brain Male	brain
21	chr6:106761200-106764400	Weak transcription	Psoas Muscle	Psoas
22	chr6:106761200-106772000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:106761400-106767200	Weak transcription	Hela-S3	cervix
24	chr6:106761400-106771400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:106761400-106771400	Weak transcription	Colonic Mucosa	Colon
26	chr6:106761400-106771800	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:106762000-106764400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:106762000-106772600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:106763000-106766000	Weak transcription	Gastric	stomach
30	chr6:106763200-106766000	Weak transcription	Left Ventricle	heart
31	chr6:106763200-106766000	Weak transcription	Right Ventricle	heart
32	chr6:106763200-106766000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:106763200-106766000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:106763200-106770800	Weak transcription	Lung	lung
35	chr6:106763200-106771200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:106763200-106771200	Weak transcription	Fetal Intestine Small	intestine
37	chr6:106763200-106771200	Weak transcription	Pancreas	Pancrea
38	chr6:106763200-106771400	Weak transcription	Fetal Kidney	kidney
39	chr6:106763200-106771800	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:106763200-106771800	Weak transcription	Fetal Stomach	stomach
41	chr6:106763400-106764400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:106763400-106764400	Weak transcription	Brain Angular Gyrus	brain
43	chr6:106763400-106766000	Weak transcription	Ovary	ovary
44	chr6:106763400-106766200	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:106763400-106771400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:106763400-106771400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:106763400-106771600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:106763400-106771800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:106763400-106771800	Weak transcription	Placenta	Placenta
50	chr6:106763400-106772400	Weak transcription	Aorta	Aorta

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