Variant report

Variant	rs11621162
Chromosome Location	chr14:78139292-78139293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78137716..78140274-chr14:78142246..78143787,2	MCF-7	breast:
2	chr14:78138709..78140424-chr14:78170369..78172653,2	MCF-7	breast:
3	chr14:78133661..78136302-chr14:78138970..78141654,2	K562	blood:

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10132900	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10143701	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10162548	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11621593	0.81[AFR][1000 genomes]
rs11622176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622293	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622411	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]
rs11622449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624052	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624063	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752262	0.82[JPT][hapmap]
rs17752428	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17752707	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17752726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752950	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17825229	0.82[JPT][hapmap]
rs17825235	0.82[JPT][hapmap]
rs17825434	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112135	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651563	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886122	0.82[JPT][hapmap]
rs4461000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464012	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45444693	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45465691	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55636050	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922310	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025136	0.88[ASN][1000 genomes]
rs56060413	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065232	1.00[ASN][1000 genomes]
rs56109335	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56339806	0.87[AFR][1000 genomes]
rs57615727	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6494	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140838	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7148685	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685214	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685216	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685219	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685222	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685223	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685230	1.00[ASN][1000 genomes]
rs72685232	1.00[ASN][1000 genomes]
rs72685238	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72685244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685246	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72685260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685273	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685281	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685297	0.81[AFR][1000 genomes]
rs72685300	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685302	0.81[AFR][1000 genomes]
rs72687205	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687216	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687217	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687218	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687223	0.81[AFR][1000 genomes]
rs72687228	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687229	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687246	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687247	0.81[AFR][1000 genomes]
rs72687250	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687251	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688824	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7492501	0.81[AFR][1000 genomes]
rs8015313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv869872	chr14:78119527-78161340	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv3693172	chr14:78130479-78152921	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv9156	chr14:78138141-78140714	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11621162	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	chr14:78121400-78139800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:78121800-78139800	Weak transcription	Gastric	stomach
3	chr14:78122000-78139600	Weak transcription	Fetal Intestine Large	intestine
4	chr14:78122000-78139800	Weak transcription	Pancreas	Pancrea
5	chr14:78125400-78139800	Weak transcription	Right Ventricle	heart
6	chr14:78126800-78139800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:78126800-78139800	Weak transcription	Spleen	Spleen
8	chr14:78127400-78139800	Weak transcription	Lung	lung
9	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:78127600-78139800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr14:78127600-78140000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:78127600-78140000	Weak transcription	Esophagus	oesophagus
13	chr14:78127800-78139600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:78127800-78139800	Weak transcription	Brain Germinal Matrix	brain
15	chr14:78128000-78157800	Weak transcription	Fetal Brain Male	brain
16	chr14:78128200-78139600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:78129000-78139800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:78129200-78139600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:78129800-78147600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr14:78130000-78139800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr14:78130200-78139400	Weak transcription	HUVEC	blood vessel
22	chr14:78130200-78139600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr14:78130400-78139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:78130400-78139400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr14:78130400-78139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:78130400-78139800	Weak transcription	Hela-S3	cervix
27	chr14:78130400-78139800	Weak transcription	NHEK	skin
28	chr14:78130400-78140200	Weak transcription	HMEC	breast
29	chr14:78130600-78139600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr14:78133400-78139800	Weak transcription	Osteobl	bone
31	chr14:78133800-78139800	Weak transcription	HSMM	muscle
32	chr14:78133800-78140400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr14:78134200-78148000	Weak transcription	NH-A	brain
34	chr14:78134400-78139800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr14:78134400-78163400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr14:78134600-78139600	Weak transcription	Brain Angular Gyrus	brain
37	chr14:78135000-78139600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr14:78135000-78140000	Weak transcription	Fetal Intestine Small	intestine
39	chr14:78135200-78139800	Weak transcription	Fetal Stomach	stomach
40	chr14:78135200-78156200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr14:78135400-78139600	Weak transcription	Thymus	Thymus
42	chr14:78136200-78139800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr14:78136200-78139800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr14:78136200-78139800	Weak transcription	NHDF-Ad	bronchial
45	chr14:78136200-78140000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr14:78136200-78148000	Weak transcription	HSMMtube	muscle
47	chr14:78136200-78162800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr14:78136600-78139400	Weak transcription	Brain Substantia Nigra	brain
49	chr14:78137200-78141000	Weak transcription	Stomach Mucosa	stomach
50	chr14:78137400-78140000	Weak transcription	A549	lung

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