Variant report

Variant	rs6678103
Chromosome Location	chr1:223966391-223966392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223964914..223967856-chr1:224032399..224034591,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10799327	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915882	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915892	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915917	0.95[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs10915946	0.81[EUR][1000 genomes]
rs10915948	0.81[EUR][1000 genomes]
rs10915956	0.81[EUR][1000 genomes]
rs1124943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11801971	0.83[EUR][1000 genomes]
rs11802505	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs11806886	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12021759	0.86[EUR][1000 genomes]
rs12021785	0.85[EUR][1000 genomes]
rs12024535	0.85[EUR][1000 genomes]
rs12026098	0.85[EUR][1000 genomes]
rs12026835	0.84[EUR][1000 genomes]
rs12027539	0.89[CEU][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs12030094	0.81[EUR][1000 genomes]
rs12038299	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12040633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12042503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045776	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12730520	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12731254	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12745879	0.80[EUR][1000 genomes]
rs17559050	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17559134	0.82[CHB][hapmap]
rs17599	0.92[EUR][1000 genomes]
rs2014441	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126389	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs2169459	0.82[EUR][1000 genomes]
rs34124959	0.85[EUR][1000 genomes]
rs35634773	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3856161	0.88[EUR][1000 genomes]
rs4653644	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs4653645	0.84[EUR][1000 genomes]
rs4653775	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56280097	0.80[EUR][1000 genomes]
rs59866505	0.81[EUR][1000 genomes]
rs61823593	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61823594	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61823595	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61824002	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61824006	0.89[EUR][1000 genomes]
rs6658752	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs6677956	0.81[EUR][1000 genomes]
rs6688246	0.85[EUR][1000 genomes]
rs6693324	0.81[EUR][1000 genomes]
rs6702843	0.86[EUR][1000 genomes]
rs723999	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs745697	0.95[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs7516059	0.86[EUR][1000 genomes]
rs7519753	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7533614	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7554109	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-223967000	Strong transcription	Lung	lung
2	chr1:223956600-223967200	Strong transcription	Colonic Mucosa	Colon
3	chr1:223956600-223968400	Strong transcription	Fetal Brain Female	brain
4	chr1:223956600-223969000	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:223956600-223969000	Strong transcription	Fetal Stomach	stomach
6	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:223956800-223969000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:223956800-223969200	Strong transcription	Placenta	Placenta
10	chr1:223956800-223974200	Strong transcription	Primary T cells from cord blood	blood
11	chr1:223956800-223974200	Strong transcription	Liver	Liver
12	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:223957200-223968000	Strong transcription	Brain Germinal Matrix	brain
14	chr1:223957200-223968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:223957200-223972800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:223959600-223966600	Weak transcription	Fetal Brain Male	brain
17	chr1:223959600-223969000	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:223959800-223977600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:223960000-223968600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:223960000-223969000	Strong transcription	Fetal Kidney	kidney
21	chr1:223960000-223972200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:223960200-223970000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:223960200-223971800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
25	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:223960400-223968800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:223960600-223967200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:223960600-223986800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:223960800-223967400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr1:223960800-223967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:223960800-223968600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:223960800-223995400	Weak transcription	GM12878-XiMat	blood
35	chr1:223961200-223966600	Strong transcription	Brain Hippocampus Middle	brain
36	chr1:223961200-223967000	Strong transcription	Brain Substantia Nigra	brain
37	chr1:223961200-223968400	Strong transcription	Fetal Lung	lung
38	chr1:223961400-223966400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:223961400-223968800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr1:223961400-223969000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:223961600-223968000	Strong transcription	Brain Anterior Caudate	brain
42	chr1:223961800-223967000	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr1:223961800-223969000	Strong transcription	Rectal Smooth Muscle	rectum
44	chr1:223961800-223972200	Strong transcription	Dnd41	blood
45	chr1:223961800-223977200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:223962000-223975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:223962600-223970600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:223962600-223983600	Weak transcription	Psoas Muscle	Psoas
50	chr1:223962800-223972600	Strong transcription	Primary B cells from cord blood	blood

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