Variant report

Variant	rs6701173
Chromosome Location	chr1:228428805-228428806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228426358..228429102-chr1:228433065..228434825,2	MCF-7	breast:
2	chr1:228426928..228429804-chr1:228442378..228444505,2	MCF-7	breast:
3	chr1:228423250..228427133-chr1:228428508..228431857,5	K562	blood:
4	chr1:228427134..228429598-chr1:228591173..228592748,2	K562	blood:

Variant related genes	Relation type
ENSG00000154358	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10158275	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1150906	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs11809443	0.85[YRI][hapmap]
rs1188697	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs12088965	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12093044	0.80[YRI][hapmap]
rs12407114	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12727512	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12728259	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12737540	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs287603	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs287604	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs287605	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs287606	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs380737	0.84[YRI][hapmap]
rs3856331	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs391597	1.00[CEU][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs395285	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs397637	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs407918	0.81[EUR][1000 genomes]
rs412716	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs424645	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs437129	0.81[EUR][1000 genomes]
rs438382	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs447902	0.81[EUR][1000 genomes]
rs453140	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs481986	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs482888	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs510931	0.91[EUR][1000 genomes]
rs540662	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs549590	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521297	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv3372505	chr1:228424229-228428827	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228413800-228429000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:228414400-228430400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:228417200-228433000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228418400-228436000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:228419600-228429600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:228422200-228434800	ZNF genes & repeats	Dnd41	blood
7	chr1:228422400-228431000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:228423600-228429800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:228424400-228429600	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr1:228424400-228430800	Strong transcription	Left Ventricle	heart
11	chr1:228424600-228429400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:228425600-228429400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:228425600-228429400	ZNF genes & repeats	Thymus	Thymus
14	chr1:228425800-228429400	ZNF genes & repeats	Fetal Thymus	thymus
15	chr1:228425800-228434200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:228426000-228429400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:228426000-228435200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr1:228426200-228429200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:228426400-228429200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:228426400-228429800	Strong transcription	Right Ventricle	heart
21	chr1:228426400-228430000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:228426600-228434400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:228426800-228429400	Strong transcription	Fetal Heart	heart
24	chr1:228426800-228429800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:228427000-228429400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:228427000-228429400	ZNF genes & repeats	Fetal Stomach	stomach
27	chr1:228427000-228430200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:228427000-228435600	ZNF genes & repeats	Brain Germinal Matrix	brain
29	chr1:228427200-228430800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:228427200-228434600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:228427400-228432000	Weak transcription	Psoas Muscle	Psoas
32	chr1:228428000-228429000	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr1:228428000-228429000	Genic enhancers	HSMMtube	muscle
34	chr1:228428000-228429200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr1:228428000-228429200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
36	chr1:228428000-228429400	ZNF genes & repeats	Fetal Brain Female	brain
37	chr1:228428000-228429400	ZNF genes & repeats	Lung	lung
38	chr1:228428000-228429600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
39	chr1:228428000-228432200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:228428000-228433400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr1:228428200-228429400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:228428200-228430800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
43	chr1:228428200-228433200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr1:228428200-228434200	ZNF genes & repeats	Fetal Lung	lung
45	chr1:228428200-228434600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:228428200-228435000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr1:228428400-228429200	ZNF genes & repeats	Esophagus	oesophagus
48	chr1:228428400-228429800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:228428400-228434000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
50	chr1:228428400-228434400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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