Variant report

Variant	rs11171730
Chromosome Location	chr12:39714610-39714611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39713760..39716372-chr12:39835448..39837014,2	MCF-7	breast:
2	chr12:39706735..39709135-chr12:39713252..39715316,2	K562	blood:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10876868	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876876	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876886	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11171674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171675	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171789	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171891	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171901	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171923	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11171938	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11830643	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11836755	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12228767	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12230604	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12424345	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1512936	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1512942	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1567739	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17127019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1828653	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1955314	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2388320	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736466	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57756176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57833783	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59695906	0.81[AMR][1000 genomes]
rs60792848	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7137143	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7953548	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7964447	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7971515	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979329	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs958914	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899013	chr12:39567945-39732430	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470286	chr12:39651893-39729700	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39686600-39722400	Weak transcription	GM12878-XiMat	blood
2	chr12:39686600-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:39686800-39729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:39686800-39738800	Weak transcription	Pancreas	Pancrea
5	chr12:39687200-39726400	Weak transcription	Fetal Intestine Small	intestine
6	chr12:39687600-39723800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:39688400-39724600	Weak transcription	Esophagus	oesophagus
8	chr12:39688400-39726400	Weak transcription	Aorta	Aorta
9	chr12:39689000-39724000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:39689600-39725400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:39690400-39715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:39695000-39726400	Weak transcription	Fetal Intestine Large	intestine
13	chr12:39695000-39726400	Weak transcription	HepG2	liver
14	chr12:39695600-39724000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:39695600-39742000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
17	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
18	chr12:39698000-39724400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:39698200-39724400	Weak transcription	K562	blood
20	chr12:39698600-39724000	Weak transcription	Brain Anterior Caudate	brain
21	chr12:39698600-39724000	Weak transcription	Brain Substantia Nigra	brain
22	chr12:39698600-39725200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:39698600-39725400	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:39699600-39724600	Weak transcription	Brain Angular Gyrus	brain
25	chr12:39699600-39760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:39700000-39721400	Weak transcription	Fetal Heart	heart
27	chr12:39700600-39723400	Weak transcription	Adipose Nuclei	Adipose
28	chr12:39700600-39724000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:39700800-39724000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:39701000-39726400	Weak transcription	Left Ventricle	heart
31	chr12:39701200-39716400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:39701400-39724000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:39701600-39716400	Weak transcription	Brain Germinal Matrix	brain
34	chr12:39701600-39718200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:39701600-39723800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr12:39701600-39723800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:39701600-39724000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:39701600-39725000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:39701800-39724400	Weak transcription	HMEC	breast
40	chr12:39704200-39746200	Weak transcription	HUVEC	blood vessel
41	chr12:39704600-39718800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:39704600-39723200	Weak transcription	NHEK	skin
43	chr12:39705800-39722200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:39710800-39724800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:39711200-39726400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:39711800-39716400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:39711800-39724000	Weak transcription	Placenta	Placenta
48	chr12:39711800-39724000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:39711800-39724000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:39712000-39714800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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