Variant report

Variant	rs4653961
Chromosome Location	chr1:228634287-228634288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228633250..228635645-chr1:228673935..228676432,2	MCF-7	breast:
2	chr1:228627994..228630263-chr1:228633987..228636188,2	MCF-7	breast:
3	chr1:228617056..228620810-chr1:228631528..228634565,4	MCF-7	breast:
4	chr1:228554896..228558917-chr1:228634186..228636261,3	K562	blood:

Variant related genes	Relation type
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10916315	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916316	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916318	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs10916319	1.00[EUR][1000 genomes]
rs12091870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16841344	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs16848618	0.89[EUR][1000 genomes]
rs2104436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291998	0.89[EUR][1000 genomes]
rs34297060	0.89[EUR][1000 genomes]
rs3738688	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4653550	0.89[EUR][1000 genomes]
rs4653952	0.89[EUR][1000 genomes]
rs4653953	0.89[EUR][1000 genomes]
rs4653957	0.89[EUR][1000 genomes]
rs4653958	0.89[EUR][1000 genomes]
rs4653963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56721656	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56895565	0.89[EUR][1000 genomes]
rs58110358	0.89[EUR][1000 genomes]
rs59225017	0.89[EUR][1000 genomes]
rs60640636	0.89[EUR][1000 genomes]
rs6679518	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6690116	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228633000-228634400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228633000-228634400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:228633000-228634600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:228633200-228634400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:228633200-228634400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:228633200-228634400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:228633200-228634400	Active TSS	Brain Angular Gyrus	brain
8	chr1:228633200-228634600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:228633200-228634800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr1:228633200-228635000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:228633400-228634400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:228633400-228634400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:228633400-228634400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:228633400-228634400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:228633400-228634400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr1:228633400-228634400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
17	chr1:228633400-228634400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
18	chr1:228633400-228634400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr1:228633400-228634400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr1:228633400-228634600	Active TSS	Brain Germinal Matrix	brain
21	chr1:228633400-228634800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:228633400-228635000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:228633600-228634400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:228633600-228634400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:228633600-228634400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:228633600-228634400	Active TSS	Right Atrium	heart
27	chr1:228633600-228635000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:228633600-228635000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:228633800-228634400	Flanking Active TSS	Right Ventricle	heart
30	chr1:228633800-228635000	Enhancers	Fetal Brain Male	brain
31	chr1:228633800-228636000	Weak transcription	K562	blood
32	chr1:228634000-228634400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:228634000-228634400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr1:228634000-228634400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:228634000-228634400	Bivalent Enhancer	Fetal Thymus	thymus
36	chr1:228634000-228634800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr1:228634000-228643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:228634200-228634400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:228634200-228634400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr1:228634200-228634400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
41	chr1:228634200-228634400	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr1:228634200-228634400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:228634200-228634400	Active TSS	Brain Anterior Caudate	brain
44	chr1:228634200-228634400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
45	chr1:228634200-228634400	Bivalent Enhancer	Placenta	Placenta
46	chr1:228634200-228634400	Enhancers	Ovary	ovary
47	chr1:228634200-228634400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
48	chr1:228634200-228634400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
49	chr1:228634200-228634400	Bivalent/Poised TSS	NH-A	brain
50	chr1:228634200-228634800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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