Variant report

Variant	rs62152908
Chromosome Location	chr2:97574592-97574593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97559950..97563991-chr2:97572149..97576823,4	K562	blood:
2	chr2:97534791..97536371-chr2:97573081..97574956,2	K562	blood:
3	chr2:97572989..97575814-chr2:97581255..97584534,3	K562	blood:
4	chr2:97572989..97575814-chr2:97581720..97584534,3	K562	blood:
5	chr2:97533515..97536291-chr2:97573456..97575907,2	K562	blood:
6	chr2:97573759..97576397-chr2:97592286..97595872,3	MCF-7	breast:
7	chr2:97572632..97575087-chr2:97615187..97616710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction
ENSG00000168758	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10191663	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11888101	0.86[EUR][1000 genomes]
rs11889101	0.97[ASN][1000 genomes]
rs11900466	0.97[ASN][1000 genomes]
rs13407036	0.94[EUR][1000 genomes]
rs17119655	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119656	0.90[EUR][1000 genomes]
rs2314651	0.83[EUR][1000 genomes]
rs28612110	0.86[EUR][1000 genomes]
rs3903548	0.97[ASN][1000 genomes]
rs4260285	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57397886	0.97[ASN][1000 genomes]
rs58232717	0.97[ASN][1000 genomes]
rs58984980	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59131346	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59660613	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60063645	0.95[ASN][1000 genomes]
rs62152900	0.92[ASN][1000 genomes]
rs62152901	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62152903	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152904	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152905	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62152906	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62152907	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62152910	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576990	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6708171	0.92[ASN][1000 genomes]
rs6717064	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718420	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6721921	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6734326	0.95[ASN][1000 genomes]
rs6734673	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746020	0.95[ASN][1000 genomes]
rs6751815	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72811651	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72811653	1.00[ASN][1000 genomes]
rs72811663	0.97[ASN][1000 genomes]
rs72811667	0.97[ASN][1000 genomes]
rs7572852	0.92[EUR][1000 genomes]
rs7589232	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7591775	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7592101	0.93[EUR][1000 genomes]
rs7603256	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62152908	FAM178B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97563400-97575200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:97565000-97575000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:97570000-97575000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:97570000-97575400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:97570200-97575000	Weak transcription	Primary T cells from cord blood	blood
6	chr2:97572000-97576000	Enhancers	Brain Substantia Nigra	brain
7	chr2:97572000-97576200	Enhancers	Brain Cingulate Gyrus	brain
8	chr2:97572200-97575800	Enhancers	Spleen	Spleen
9	chr2:97572200-97576000	Enhancers	Brain Angular Gyrus	brain
10	chr2:97572200-97576400	Enhancers	Left Ventricle	heart
11	chr2:97572400-97579200	Enhancers	Fetal Brain Male	brain
12	chr2:97573200-97575800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:97573200-97578000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:97573400-97574800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr2:97573400-97576000	Enhancers	Right Ventricle	heart
16	chr2:97573600-97575400	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr2:97573600-97577800	Weak transcription	K562	blood
18	chr2:97573600-97578000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:97573800-97575000	Weak transcription	Fetal Brain Female	brain
20	chr2:97573800-97575400	Enhancers	Adipose Nuclei	Adipose
21	chr2:97573800-97575800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:97573800-97575800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:97573800-97577600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:97573800-97577600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:97573800-97579000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:97574000-97575000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:97574000-97575000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:97574000-97575000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:97574000-97575000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:97574000-97575200	Weak transcription	Right Atrium	heart
31	chr2:97574000-97575400	Enhancers	Fetal Muscle Leg	muscle
32	chr2:97574000-97575400	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:97574000-97577200	Weak transcription	Brain Germinal Matrix	brain
34	chr2:97574000-97577400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:97574000-97578000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:97574000-97578000	Weak transcription	Lung	lung
37	chr2:97574000-97578200	Weak transcription	Esophagus	oesophagus
38	chr2:97574000-97578200	Weak transcription	Fetal Thymus	thymus
39	chr2:97574000-97578600	Weak transcription	Placenta	Placenta
40	chr2:97574000-97582000	Weak transcription	Colonic Mucosa	Colon
41	chr2:97574200-97575000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:97574200-97575600	Enhancers	Colon Smooth Muscle	Colon
43	chr2:97574200-97577600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:97574200-97577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:97574200-97578200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:97574200-97578400	Weak transcription	Pancreas	Pancrea
47	chr2:97574400-97574800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:97574400-97574800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:97574400-97575200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:97574400-97575200	Enhancers	Fetal Heart	heart

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