Variant report

Variant	rs4149871
Chromosome Location	chr1:242017475-242017476
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	chr1:242011331..242013825-chr1:242014909..242017779,3	MCF-7	breast:
2	chr1:241871145..241872742-chr1:242017335..242019285,2	K562	blood:

Variant related genes	Relation type
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12138714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298931	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298932	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298933	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35245437	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3819355	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819356	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819357	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819359	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819360	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4149852	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149855	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149889	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149890	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149891	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149927	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149963	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv873373	chr1:241939069-242027500	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv873374	chr1:241975147-242097624	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv1008886	chr1:242015591-242176983	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242012000-242021400	Weak transcription	Right Atrium	heart
2	chr1:242012000-242023800	Weak transcription	Stomach Mucosa	stomach
3	chr1:242012000-242032600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:242012200-242025600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:242012200-242027800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:242012200-242028600	Weak transcription	Gastric	stomach
7	chr1:242012200-242044000	Weak transcription	Primary B cells from cord blood	blood
8	chr1:242012400-242019400	Weak transcription	Fetal Brain Male	brain
9	chr1:242012400-242060200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:242012600-242023200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:242012600-242051600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:242012600-242051800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:242012800-242019800	Weak transcription	Fetal Kidney	kidney
14	chr1:242012800-242020600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:242012800-242054600	Weak transcription	HSMM	muscle
16	chr1:242012800-242056000	Weak transcription	Fetal Intestine Small	intestine
17	chr1:242013000-242053400	Weak transcription	Fetal Lung	lung
18	chr1:242013200-242017800	Weak transcription	Esophagus	oesophagus
19	chr1:242013200-242018200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:242013200-242018400	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr1:242013200-242018600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:242013200-242020400	Weak transcription	HUVEC	blood vessel
23	chr1:242013200-242022000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:242013200-242023800	Weak transcription	NH-A	brain
25	chr1:242013200-242028800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:242013200-242030000	Weak transcription	NHDF-Ad	bronchial
27	chr1:242013200-242030200	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:242013200-242032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:242013200-242034200	Weak transcription	Brain Germinal Matrix	brain
30	chr1:242013200-242036600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:242013200-242038800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:242013200-242042000	Weak transcription	HepG2	liver
33	chr1:242013200-242048000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:242013200-242053200	Weak transcription	Osteobl	bone
35	chr1:242013200-242056400	Weak transcription	NHLF	lung
36	chr1:242013400-242018400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:242013400-242049400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:242013400-242055800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:242013600-242038600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:242013600-242039000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:242014000-242018200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:242014400-242018200	Strong transcription	Hela-S3	cervix
43	chr1:242014600-242017800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:242014600-242018000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:242014600-242018200	Strong transcription	Fetal Thymus	thymus
46	chr1:242014800-242018200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:242014800-242034400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:242015000-242018000	Strong transcription	A549	lung
49	chr1:242015000-242018200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:242015000-242018400	Strong transcription	K562	blood

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