Variant report

Variant	rs2236246
Chromosome Location	chr14:104379206-104379207
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104377058..104380322-chr14:104382660..104385611,3	MCF-7	breast:
2	chr14:104268895..104271672-chr14:104378681..104380449,2	MCF-7	breast:
3	chr14:104379142..104381534-chr14:104393675..104395664,2	K562	blood:
4	chr14:104375126..104376640-chr14:104376755..104379317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156411	Chromatin interaction
ENSG00000156414	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10136440	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10149651	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11622475	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap]
rs11625697	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs1187446	0.89[AMR][1000 genomes]
rs1187448	0.87[AMR][1000 genomes]
rs12885873	0.95[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap]
rs12889168	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs12895359	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12895592	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17101911	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1885072	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2005081	0.84[AMR][1000 genomes]
rs2236247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273610	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2368984	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34288430	0.85[AMR][1000 genomes]
rs34964872	0.84[AMR][1000 genomes]
rs36032081	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56060232	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59776579	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6576012	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7143682	0.89[AMR][1000 genomes]
rs7143936	0.81[AMR][1000 genomes]
rs7145167	0.85[ASN][1000 genomes]
rs743212	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8021692	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs941946	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
7	nsv1042792	chr14:104326137-104384260	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv542207	chr14:104326137-104384260	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1048353	chr14:104361402-104483286	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv902322	chr14:104365310-104464809	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2236246	TDRD9	cis	lung	GTEx
rs2236246	TDRD9	cis	parietal	SCAN
rs2236246	TDRD9	cis	Artery Tibial	GTEx
rs2236246	TDRD9	cis	Adipose Subcutaneous	GTEx
rs2236246	ZFYVE21	cis	cerebellum	SCAN
rs2236246	TDRD9	cis	multi-tissue	Pritchard
rs2236246	C14orf2	cis	cerebellum	SCAN
rs2236246	TDRD9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104363200-104387000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:104375000-104385800	Weak transcription	Small Intestine	intestine
3	chr14:104375800-104384200	Strong transcription	Dnd41	blood
4	chr14:104376000-104384800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr14:104376600-104384200	Weak transcription	Right Atrium	heart
6	chr14:104376800-104382200	Weak transcription	Pancreas	Pancrea
7	chr14:104376800-104386200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr14:104376800-104387000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr14:104376800-104387000	Weak transcription	Stomach Mucosa	stomach
10	chr14:104377200-104379800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr14:104377200-104380400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr14:104377200-104384800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:104377200-104385600	Strong transcription	Fetal Intestine Small	intestine
14	chr14:104377200-104386400	Weak transcription	Fetal Heart	heart
15	chr14:104377200-104386800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr14:104377400-104379400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr14:104377400-104379600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:104377400-104380200	Strong transcription	Brain Cingulate Gyrus	brain
19	chr14:104377400-104380200	Strong transcription	Esophagus	oesophagus
20	chr14:104377400-104380400	Strong transcription	Brain Hippocampus Middle	brain
21	chr14:104377400-104380600	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr14:104377400-104380800	Strong transcription	Primary T cells from cord blood	blood
23	chr14:104377400-104381000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr14:104377400-104381000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr14:104377400-104381000	Strong transcription	Right Ventricle	heart
26	chr14:104377400-104381200	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr14:104377400-104381400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:104377400-104381600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr14:104377400-104381800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr14:104377400-104383000	Strong transcription	Adipose Nuclei	Adipose
31	chr14:104377400-104383200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:104377400-104383200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:104377400-104383800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr14:104377400-104384400	Strong transcription	Placenta	Placenta
35	chr14:104377400-104384600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr14:104377400-104384600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr14:104377400-104384600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr14:104377400-104384600	Strong transcription	Liver	Liver
39	chr14:104377400-104384600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr14:104377400-104384600	Strong transcription	Fetal Intestine Large	intestine
41	chr14:104377400-104384600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr14:104377400-104384600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr14:104377400-104384800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr14:104377400-104384800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:104377400-104384800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr14:104377400-104384800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr14:104377400-104384800	Strong transcription	Thymus	Thymus
48	chr14:104377400-104385200	Strong transcription	Fetal Brain Female	brain
49	chr14:104377400-104385200	Strong transcription	Fetal Muscle Leg	muscle
50	chr14:104377400-104386000	Strong transcription	Fetal Stomach	stomach

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