Variant report

Variant	rs17751876
Chromosome Location	chr14:78055653-78055654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12431896	1.00[ASW][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12433198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176895	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs176896	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs176899	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs176906	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs176908	1.00[ASW][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs176911	1.00[AFR][1000 genomes]
rs176912	0.83[AMR][1000 genomes]
rs17751917	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17751923	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17751980	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17751993	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17752165	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17752707	1.00[MKK][hapmap]
rs17824984	0.81[CEU][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17825014	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2142187	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2178877	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2299918	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364578	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2886132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4497612	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55697089	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55776552	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs55799811	1.00[AFR][1000 genomes]
rs56264628	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs56286233	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	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
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17751876	ADCK1	cis	Whole Blood	GTEx
rs17751876	SPTLC2	cis	Nerve Tibial	GTEx
rs17751876	ADCK1	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:78016400-78061000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:78021800-78061000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
7	chr14:78022000-78060800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:78030200-78056800	Weak transcription	HMEC	breast
9	chr14:78042400-78059000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:78042400-78060800	Weak transcription	Aorta	Aorta
11	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
12	chr14:78042600-78061800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr14:78043000-78059800	Weak transcription	A549	lung
14	chr14:78043200-78058800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr14:78043800-78060800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr14:78043800-78061000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:78043800-78061200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr14:78043800-78061800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr14:78044000-78060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr14:78044000-78061000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr14:78044000-78061200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr14:78044600-78061000	Weak transcription	Thymus	Thymus
23	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
24	chr14:78047600-78059600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr14:78047800-78059800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr14:78047800-78061000	Weak transcription	Brain Germinal Matrix	brain
27	chr14:78048000-78056600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:78048000-78059800	Weak transcription	K562	blood
29	chr14:78048000-78061400	Weak transcription	Fetal Intestine Small	intestine
30	chr14:78048200-78056400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr14:78048200-78056400	Weak transcription	NHEK	skin
32	chr14:78048200-78056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr14:78048200-78057200	Weak transcription	Fetal Intestine Large	intestine
34	chr14:78048200-78059600	Weak transcription	NH-A	brain
35	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
36	chr14:78049200-78059600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr14:78049200-78059800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr14:78049400-78059600	Weak transcription	Osteobl	bone
39	chr14:78049400-78059800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:78049400-78060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr14:78049400-78061000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr14:78049600-78061000	Weak transcription	Fetal Muscle Leg	muscle
44	chr14:78050000-78057200	Weak transcription	Small Intestine	intestine
45	chr14:78050800-78061000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr14:78051000-78057200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr14:78051400-78057800	Weak transcription	Right Atrium	heart
48	chr14:78051400-78059600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr14:78051400-78061400	Weak transcription	Esophagus	oesophagus
50	chr14:78051400-78061800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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