Variant report

Variant	rs1222156
Chromosome Location	chr1:223952152-223952153
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223948378..223951598-chr1:223951905..223956257,3	MCF-7	breast:
2	chr1:223944085..223948831-chr1:223951617..223954672,7	K562	blood:
3	chr1:223950388..223952525-chr1:223958515..223960018,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1153927	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1153929	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1153930	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1153933	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1153934	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1153936	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1153937	0.82[AMR][1000 genomes]
rs1153938	0.82[AMR][1000 genomes]
rs1153943	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1153947	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1153949	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1153971	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1153973	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1222120	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1222121	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1222124	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1222128	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1222146	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1621129	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1629850	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842270	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16842294	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1981171	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1982610	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1982612	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1982613	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2242188	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28370163	0.89[EUR][1000 genomes]
rs28370164	0.89[EUR][1000 genomes]
rs28370167	0.89[EUR][1000 genomes]
rs28370172	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738370	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3767709	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3820475	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653457	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56329085	0.85[EUR][1000 genomes]
rs56918361	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59104475	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59196624	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60131749	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60164080	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6675712	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6687003	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694214	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72749554	0.83[EUR][1000 genomes]
rs72749569	0.83[EUR][1000 genomes]
rs737066	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750873	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536779	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription 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 target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers 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	36 gene(s)	inside rSNPs	diseases
9	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223954400	Strong transcription	HSMM	muscle
6	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
7	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
8	chr1:223937000-223954400	Strong transcription	Gastric	stomach
9	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
14	chr1:223937000-223954800	Strong transcription	Osteobl	bone
15	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
18	chr1:223937200-223952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:223937200-223953000	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:223937200-223954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:223937200-223954800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:223937200-223954800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:223937200-223954800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
26	chr1:223937400-223952600	Strong transcription	NH-A	brain
27	chr1:223937400-223952800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr1:223937400-223952800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:223937400-223953000	Strong transcription	Adipose Nuclei	Adipose
30	chr1:223937400-223954400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:223937400-223954400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:223937400-223954400	Strong transcription	NHLF	lung
33	chr1:223937400-223954800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:223937400-223954800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:223937400-223954800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:223937400-223954800	Strong transcription	Fetal Stomach	stomach
37	chr1:223937400-223954800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:223937400-223954800	Strong transcription	A549	lung
39	chr1:223937600-223954200	Strong transcription	Left Ventricle	heart
40	chr1:223937600-223954800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr1:223937800-223954800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:223937800-223954800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:223938000-223953000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:223938000-223954200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr1:223938000-223954800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:223938000-223954800	Strong transcription	Fetal Brain Female	brain
47	chr1:223938200-223954200	Strong transcription	Brain Germinal Matrix	brain
48	chr1:223938200-223954400	Strong transcription	Ovary	ovary
49	chr1:223938200-223954400	Strong transcription	Spleen	Spleen
50	chr1:223938200-223954800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links