Variant report

Variant	rs348189
Chromosome Location	chr1:155653948-155653949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155639842..155641507-chr1:155653643..155656160,2	MCF-7	breast:
2	chr1:155644991..155647996-chr1:155653884..155656777,3	MCF-7	breast:
3	chr1:155650232..155654143-chr1:155656732..155660370,8	MCF-7	breast:
4	chr1:155646937..155653370-chr1:155653884..155660272,11	K562	blood:
5	chr1:155652988..155656346-chr1:155657323..155660504,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163374	Chromatin interaction
ENSG00000132676	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10796951	0.95[AFR][1000 genomes]
rs10796952	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802649	0.81[AMR][1000 genomes]
rs12136836	0.92[AFR][1000 genomes]
rs1625821	0.89[AMR][1000 genomes]
rs1627630	0.89[AMR][1000 genomes]
rs168343	0.89[AMR][1000 genomes]
rs171168	0.89[AMR][1000 genomes]
rs1749412	0.89[AMR][1000 genomes]
rs1749413	0.89[AMR][1000 genomes]
rs1749414	0.89[AMR][1000 genomes]
rs1749420	0.89[AMR][1000 genomes]
rs1749422	0.89[AMR][1000 genomes]
rs1756242	0.89[AMR][1000 genomes]
rs182979	0.81[AMR][1000 genomes]
rs1886618	0.89[AMR][1000 genomes]
rs2136920	0.89[AMR][1000 genomes]
rs2175389	0.89[AMR][1000 genomes]
rs2363017	0.89[AMR][1000 genomes]
rs2485472	0.89[AMR][1000 genomes]
rs2666828	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2686264	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2885676	0.89[AMR][1000 genomes]
rs348184	0.89[AMR][1000 genomes]
rs348188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348190	0.81[AMR][1000 genomes]
rs348191	0.89[AMR][1000 genomes]
rs348194	0.81[AMR][1000 genomes]
rs348197	0.89[AMR][1000 genomes]
rs348199	0.89[AMR][1000 genomes]
rs348200	0.89[AMR][1000 genomes]
rs348207	0.89[AMR][1000 genomes]
rs348208	0.89[AMR][1000 genomes]
rs348209	0.89[AMR][1000 genomes]
rs35264557	1.00[AMR][1000 genomes]
rs4581273	0.89[AMR][1000 genomes]
rs4601579	0.81[AFR][1000 genomes]
rs4638121	0.89[AFR][1000 genomes]
rs485353	0.83[AFR][1000 genomes]
rs492669	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4971057	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4971058	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs512551	0.89[AMR][1000 genomes]
rs540380	0.89[AMR][1000 genomes]
rs568672	0.89[AMR][1000 genomes]
rs606755	0.89[AMR][1000 genomes]
rs607036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs617232	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6427281	0.89[AFR][1000 genomes]
rs6427282	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6688399	0.89[AMR][1000 genomes]
rs670787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs683121	0.81[AMR][1000 genomes]
rs708607	0.89[AMR][1000 genomes]
rs708609	0.89[AMR][1000 genomes]
rs7522259	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7540642	0.87[AFR][1000 genomes]
rs7543447	0.81[AFR][1000 genomes]
rs8179457	0.89[AMR][1000 genomes]
rs822013	0.89[AMR][1000 genomes]
rs822014	0.89[AMR][1000 genomes]
rs822017	0.89[AMR][1000 genomes]
rs822021	0.89[AMR][1000 genomes]
rs822023	0.89[AMR][1000 genomes]
rs822024	0.89[AMR][1000 genomes]
rs822027	0.89[AMR][1000 genomes]
rs822479	0.89[AMR][1000 genomes]
rs822481	0.89[AMR][1000 genomes]
rs822483	0.89[AMR][1000 genomes]
rs822485	0.89[AMR][1000 genomes]
rs822492	0.89[AMR][1000 genomes]
rs822498	0.89[AMR][1000 genomes]
rs822522	0.89[AMR][1000 genomes]
rs866603	0.89[AMR][1000 genomes]
rs9426928	0.91[AFR][1000 genomes]
rs9427219	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427221	0.81[AMR][1000 genomes]
rs9427222	0.89[AMR][1000 genomes]
rs9427227	0.89[AMR][1000 genomes]
rs9427229	0.89[AMR][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	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	nsv3054	chr1:155653835-155673509	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155627000-155657600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:155627200-155654000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:155628000-155654600	Strong transcription	Fetal Thymus	thymus
4	chr1:155632800-155656200	Weak transcription	Stomach Mucosa	stomach
5	chr1:155634600-155657800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:155645000-155656200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:155645200-155657200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:155645400-155655600	Weak transcription	Psoas Muscle	Psoas
9	chr1:155646000-155655000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:155646200-155654200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:155646600-155655600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:155646600-155656000	Weak transcription	Lung	lung
13	chr1:155646600-155657600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:155647400-155656200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:155648200-155656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:155648600-155656400	Weak transcription	Fetal Kidney	kidney
17	chr1:155648600-155657200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:155648800-155654200	Strong transcription	Fetal Stomach	stomach
19	chr1:155648800-155654800	Strong transcription	Fetal Intestine Small	intestine
20	chr1:155648800-155656200	Weak transcription	NHDF-Ad	bronchial
21	chr1:155649600-155655200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:155649600-155656200	Weak transcription	HSMMtube	muscle
23	chr1:155649600-155656200	Weak transcription	NH-A	brain
24	chr1:155649800-155655400	Weak transcription	Osteobl	bone
25	chr1:155649800-155656000	Weak transcription	HUVEC	blood vessel
26	chr1:155650000-155657400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:155650000-155657600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:155650200-155654000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:155650200-155655400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:155650200-155656200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:155650200-155656400	Weak transcription	HSMM	muscle
32	chr1:155650200-155656800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:155650200-155657400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:155650400-155655000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:155650400-155655000	Weak transcription	Fetal Brain Female	brain
36	chr1:155650400-155655000	Weak transcription	Hela-S3	cervix
37	chr1:155650400-155655200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:155650400-155655600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:155650400-155655600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:155650400-155655600	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:155650400-155655600	Weak transcription	Fetal Lung	lung
42	chr1:155650400-155656200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:155650400-155656200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:155650400-155657200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:155650600-155654400	Weak transcription	Thymus	Thymus
46	chr1:155650600-155654800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:155650600-155655000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:155650600-155655000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:155650600-155655600	Weak transcription	Colonic Mucosa	Colon
50	chr1:155650600-155655600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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