Variant report

Variant	rs11622411
Chromosome Location	chr14:78179424-78179425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78179028..78181714-chr14:78184797..78186792,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10162548	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11621162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621593	0.80[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs11622176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624063	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752428	1.00[CHB][hapmap]
rs17752707	1.00[CHB][hapmap]
rs17752726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111829	0.80[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2112135	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651563	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45444693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45465691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55636050	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025136	0.88[ASN][1000 genomes]
rs56060413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065232	1.00[ASN][1000 genomes]
rs56109335	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56339806	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57615727	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493	0.80[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140838	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7148685	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685214	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685216	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685219	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685222	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685223	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685230	1.00[ASN][1000 genomes]
rs72685232	1.00[ASN][1000 genomes]
rs72685238	0.87[AFR][1000 genomes]
rs72685244	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685246	0.87[AFR][1000 genomes]
rs72685260	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685297	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72685300	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685302	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687218	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687223	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687228	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687229	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687246	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687247	0.87[AFR][1000 genomes]
rs72687250	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687251	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688824	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015796	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS 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	26 gene(s)	inside rSNPs	diseases
7	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11622411	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78175400-78180400	Weak transcription	Gastric	stomach
2	chr14:78175600-78180400	Weak transcription	Aorta	Aorta
3	chr14:78175600-78182200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:78176000-78179800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:78176200-78179800	Strong transcription	Primary hematopoietic stem cells	blood
6	chr14:78176200-78185400	Weak transcription	Fetal Heart	heart
7	chr14:78176200-78206000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:78176200-78208400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr14:78176200-78224000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr14:78176200-78225400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:78176400-78206200	Strong transcription	Fetal Thymus	thymus
12	chr14:78176400-78223400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:78176400-78224200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr14:78176600-78179800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
15	chr14:78176600-78180000	Strong transcription	NHDF-Ad	bronchial
16	chr14:78176600-78180400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr14:78176600-78181000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr14:78176600-78182000	Strong transcription	Primary T cells from cord blood	blood
19	chr14:78176600-78182400	Strong transcription	HUVEC	blood vessel
20	chr14:78176600-78187200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr14:78176600-78187200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr14:78176600-78197400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr14:78176600-78204600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr14:78176600-78205200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr14:78176600-78205400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr14:78176600-78205600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr14:78176600-78205600	Strong transcription	Adipose Nuclei	Adipose
28	chr14:78176600-78205800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr14:78176600-78213200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:78176600-78223200	Strong transcription	Fetal Muscle Leg	muscle
31	chr14:78176600-78224200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr14:78176800-78179600	Strong transcription	Ovary	ovary
33	chr14:78176800-78180600	Strong transcription	Fetal Lung	lung
34	chr14:78176800-78181800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr14:78176800-78181800	Strong transcription	NHEK	skin
36	chr14:78176800-78182000	Strong transcription	Primary B cells from cord blood	blood
37	chr14:78176800-78182000	Strong transcription	NH-A	brain
38	chr14:78176800-78182200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:78176800-78182400	Strong transcription	A549	lung
40	chr14:78176800-78183800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr14:78176800-78190200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:78176800-78191400	Weak transcription	Fetal Brain Male	brain
43	chr14:78176800-78192800	Strong transcription	Osteobl	bone
44	chr14:78176800-78205200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr14:78176800-78205600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr14:78176800-78205600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr14:78176800-78205600	Strong transcription	Placenta	Placenta
48	chr14:78176800-78205800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr14:78176800-78206200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr14:78176800-78207400	Strong transcription	Rectal Mucosa Donor 29	rectum

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