Variant report

Variant	rs17119655
Chromosome Location	chr2:97577495-97577496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97523464..97526230-chr2:97576942..97579887,2	K562	blood:
2	chr2:97553127..97553990-chr2:97577295..97577812,2	K562	blood:
3	chr2:97575476..97578400-chr2:97584018..97588039,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213337	Chromatin interaction
ENSG00000163126	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10191663	0.98[EUR][1000 genomes]
rs11888101	0.86[EUR][1000 genomes]
rs11889101	0.97[ASN][1000 genomes]
rs11900466	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1320147	0.82[GIH][hapmap]
rs13403225	0.82[GIH][hapmap]
rs13407036	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs17119656	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2314651	0.83[EUR][1000 genomes]
rs28612110	0.86[EUR][1000 genomes]
rs3903548	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4260285	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57397886	0.97[ASN][1000 genomes]
rs58232717	0.97[ASN][1000 genomes]
rs58984980	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59131346	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59660613	0.97[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	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62152903	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152904	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152905	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62152906	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62152907	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62152908	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576990	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs6576996	0.90[GIH][hapmap];0.80[MEX][hapmap]
rs6708171	0.92[ASN][1000 genomes]
rs6717064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718420	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6721921	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6734326	0.95[ASN][1000 genomes]
rs6734673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735969	0.85[CEU][hapmap]
rs6746020	0.95[ASN][1000 genomes]
rs6751815	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72811651	0.92[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	1.00[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7591775	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7592101	0.93[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs7593754	0.90[GIH][hapmap]
rs7603256	0.93[CEU][hapmap];0.86[EUR][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	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	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
10	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
11	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17119655	FAM178B	cis	Artery Tibial	GTEx
rs17119655	FAM178B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97572400-97579200	Enhancers	Fetal Brain Male	brain
2	chr2:97573200-97578000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:97573600-97577800	Weak transcription	K562	blood
4	chr2:97573600-97578000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:97573800-97577600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:97573800-97577600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:97573800-97579000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:97574000-97578000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:97574000-97578000	Weak transcription	Lung	lung
10	chr2:97574000-97578200	Weak transcription	Esophagus	oesophagus
11	chr2:97574000-97578200	Weak transcription	Fetal Thymus	thymus
12	chr2:97574000-97578600	Weak transcription	Placenta	Placenta
13	chr2:97574000-97582000	Weak transcription	Colonic Mucosa	Colon
14	chr2:97574200-97577600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:97574200-97577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:97574200-97578200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:97574200-97578400	Weak transcription	Pancreas	Pancrea
18	chr2:97575400-97577600	Weak transcription	Primary T cells from cord blood	blood
19	chr2:97575400-97577800	Weak transcription	Adipose Nuclei	Adipose
20	chr2:97575400-97579200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:97575600-97581600	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:97575800-97577600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:97575800-97577600	Weak transcription	Spleen	Spleen
24	chr2:97575800-97578600	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:97575800-97581800	Weak transcription	Right Atrium	heart
26	chr2:97576000-97578800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:97576000-97581600	Weak transcription	Brain Substantia Nigra	brain
28	chr2:97576200-97578200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:97576400-97578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:97576800-97578400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:97576800-97578600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr2:97576800-97578600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr2:97576800-97580600	Enhancers	Left Ventricle	heart
34	chr2:97577000-97577600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:97577000-97577600	Weak transcription	Brain Angular Gyrus	brain
36	chr2:97577000-97577600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:97577000-97577600	Enhancers	Stomach Smooth Muscle	stomach
38	chr2:97577000-97578400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:97577000-97578600	Enhancers	Fetal Brain Female	brain
40	chr2:97577000-97580600	Enhancers	Right Ventricle	heart
41	chr2:97577200-97578200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:97577200-97578600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:97577200-97578600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr2:97577200-97578800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:97577200-97580200	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr2:97577200-97589600	Weak transcription	Fetal Heart	heart
47	chr2:97577400-97577600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:97577400-97578200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr2:97577400-97578400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:97577400-97578600	Enhancers	H1 Cell Line	embryonic stem cell

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