Variant report

Variant	rs34401601
Chromosome Location	chr16:71769562-71769563
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71760087..71762768-chr16:71767472..71770185,3	MCF-7	breast:
2	chr16:71757196..71759664-chr16:71766555..71771218,5	MCF-7	breast:
3	chr16:71756712..71759795-chr16:71768156..71771579,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000040199	Chromatin interaction
ENSG00000260612	Chromatin interaction
ENSG00000261513	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1035545	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10500559	0.84[EUR][1000 genomes]
rs1058747	0.82[EUR][1000 genomes]
rs11075900	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11075902	0.88[EUR][1000 genomes]
rs11539980	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11641873	0.92[EUR][1000 genomes]
rs11645467	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11646635	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11646748	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11648674	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12051443	0.82[EUR][1000 genomes]
rs12051449	0.82[EUR][1000 genomes]
rs12051506	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12447856	0.90[EUR][1000 genomes]
rs12448226	0.86[EUR][1000 genomes]
rs12597065	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12598902	0.81[EUR][1000 genomes]
rs12920243	0.89[EUR][1000 genomes]
rs12924258	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12925587	0.85[EUR][1000 genomes]
rs12926987	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12927320	0.82[EUR][1000 genomes]
rs12930206	0.89[EUR][1000 genomes]
rs12932850	0.82[EUR][1000 genomes]
rs12935426	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1392483	0.87[EUR][1000 genomes]
rs1392487	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2036337	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2036338	0.92[EUR][1000 genomes]
rs2270830	0.92[EUR][1000 genomes]
rs2270831	0.92[EUR][1000 genomes]
rs2270832	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2278031	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2303224	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2303225	0.82[EUR][1000 genomes]
rs2334879	0.80[EUR][1000 genomes]
rs28439683	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28582831	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28636800	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28704189	0.86[EUR][1000 genomes]
rs34161748	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34734042	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34764568	0.80[EUR][1000 genomes]
rs35173463	0.92[EUR][1000 genomes]
rs3751817	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3752681	0.82[EUR][1000 genomes]
rs3925658	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4788442	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4788549	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4788551	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4788552	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4788554	0.92[EUR][1000 genomes]
rs4788558	0.86[EUR][1000 genomes]
rs4788821	0.81[EUR][1000 genomes]
rs4788826	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4788827	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57997630	0.84[EUR][1000 genomes]
rs60881203	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62053107	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62053108	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7185997	0.90[EUR][1000 genomes]
rs7404381	0.89[EUR][1000 genomes]
rs8048057	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8048210	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8052489	0.86[EUR][1000 genomes]
rs8052999	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8060867	0.89[EUR][1000 genomes]
rs8062441	0.87[EUR][1000 genomes]
rs8062477	0.88[EUR][1000 genomes]
rs8203	0.82[EUR][1000 genomes]
rs918721	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs951453	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs951939	0.88[EUR][1000 genomes]
rs9921270	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9922054	0.87[EUR][1000 genomes]
rs9925069	0.86[EUR][1000 genomes]
rs9925228	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9927336	0.86[EUR][1000 genomes]
rs9927437	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9931717	0.85[EUR][1000 genomes]
rs9936903	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9937280	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9939455	0.90[EUR][1000 genomes]
rs9940217	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9940990	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers 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 target site	56 gene(s)	inside rSNPs	diseases
2	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS 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	15 gene(s)	inside rSNPs	diseases
3	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	esv1819402	chr16:71755852-71816899	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71758400-71771000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:71758600-71776800	Weak transcription	Fetal Heart	heart
3	chr16:71761000-71805600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:71761800-71778800	Weak transcription	Small Intestine	intestine
5	chr16:71762200-71811400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:71762600-71774400	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr16:71763200-71799800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr16:71763200-71812600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr16:71763400-71769600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:71763400-71774600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr16:71763400-71776000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr16:71763400-71802200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr16:71763600-71769800	Strong transcription	GM12878-XiMat	blood
14	chr16:71763600-71784400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr16:71763600-71786200	Strong transcription	Osteobl	bone
16	chr16:71763600-71793000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr16:71763600-71800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:71763600-71801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr16:71763600-71812400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr16:71763800-71799600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr16:71763800-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr16:71764000-71769600	Strong transcription	Thymus	Thymus
23	chr16:71764000-71769600	Strong transcription	NHLF	lung
24	chr16:71764000-71774400	Strong transcription	Primary T cells from cord blood	blood
25	chr16:71764000-71784200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr16:71764000-71785200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr16:71764000-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr16:71764000-71813000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr16:71764200-71769800	Strong transcription	Adipose Nuclei	Adipose
30	chr16:71764200-71784400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr16:71764400-71782000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr16:71764400-71784400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr16:71764400-71784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr16:71764600-71769800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr16:71764600-71784600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr16:71764800-71774400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr16:71764800-71802600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr16:71765000-71774600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr16:71765400-71770000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr16:71765600-71769800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr16:71765600-71769800	Strong transcription	Fetal Lung	lung
42	chr16:71765600-71785200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr16:71766200-71774400	Strong transcription	Fetal Stomach	stomach
44	chr16:71767000-71771200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:71767000-71771200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr16:71767000-71778600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr16:71767000-71784600	Strong transcription	Fetal Muscle Leg	muscle
48	chr16:71767000-71787400	Weak transcription	Stomach Mucosa	stomach
49	chr16:71767200-71770600	Weak transcription	Colonic Mucosa	Colon
50	chr16:71767200-71770800	Weak transcription	Fetal Brain Male	brain

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