Variant report

Variant	rs17128684
Chromosome Location	chr14:56153987-56153988
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:56102256..56103857-chr14:56152714..56154637,2	K562	blood:
2	chr14:56152134..56154942-chr14:56705477..56707691,2	K562	blood:
3	chr14:56145095..56147248-chr14:56151830..56154443,3	K562	blood:
4	chr14:56145481..56148002-chr14:56152406..56155008,3	K562	blood:

Variant related genes	Relation type
ENSG00000126777	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10136408	0.86[CEU][hapmap]
rs10444721	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10483644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10483649	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10483651	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12432344	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12432588	0.82[EUR][1000 genomes]
rs12432887	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12433592	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12434609	0.92[ASN][1000 genomes]
rs12434624	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12434660	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12434799	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12435643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587700	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587705	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587735	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs12588172	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12588185	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12589864	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12589867	0.83[EUR][1000 genomes]
rs12590388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12590936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12882850	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12885864	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12891129	0.95[ASN][1000 genomes]
rs12891489	0.86[CEU][hapmap]
rs12893162	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12895070	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12895366	0.95[ASN][1000 genomes]
rs12897227	0.81[JPT][hapmap]
rs17128610	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17128614	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17128655	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17128657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17128677	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17128690	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17253737	0.95[ASN][1000 genomes]
rs17684916	0.93[ASN][1000 genomes]
rs17684959	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs17685650	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1951887	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs1951889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1951890	0.94[CEU][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2252189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274079	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296182	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2296183	0.95[ASN][1000 genomes]
rs2341889	0.82[EUR][1000 genomes]
rs28458791	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28581272	0.86[ASN][1000 genomes]
rs28703642	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34023572	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34111199	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34118806	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34133022	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34184813	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34408323	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34548095	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34697059	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34706911	0.92[ASN][1000 genomes]
rs34709110	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34853759	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34931260	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34982220	0.95[ASN][1000 genomes]
rs35047443	0.86[EUR][1000 genomes]
rs35094494	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35420484	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35451981	0.83[EUR][1000 genomes]
rs35531912	0.84[EUR][1000 genomes]
rs35535838	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35560341	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35790844	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3765515	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4457912	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs55760841	0.83[EUR][1000 genomes]
rs55927221	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56229542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60233569	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61381603	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6573051	0.82[ASN][1000 genomes]
rs6573053	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6573054	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7150285	0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7156566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7158176	0.95[ASN][1000 genomes]
rs8003149	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8006443	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8007832	0.82[MEX][hapmap]
rs8015588	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832804	chr14:56083850-56277632	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1283	chr14:56120059-56164729	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17128684	GCH1	cis	parietal	SCAN
rs17128684	KTN1	cis	parietal	SCAN
rs17128684	KTN1	cis	cerebellum	SCAN
rs17128684	NAA30	cis	cerebellum	SCAN
rs17128684	GCH1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56097600-56155400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr14:56101800-56162800	Weak transcription	Brain Germinal Matrix	brain
3	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
4	chr14:56104800-56157400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:56109200-56164000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:56113800-56155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr14:56115000-56155000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr14:56122400-56164800	Weak transcription	Small Intestine	intestine
9	chr14:56134000-56155000	Strong transcription	HSMM	muscle
10	chr14:56134600-56154200	Strong transcription	Liver	Liver
11	chr14:56136600-56154200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr14:56136800-56154200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr14:56137000-56154200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr14:56137200-56154000	Strong transcription	Primary B cells from cord blood	blood
15	chr14:56137400-56154800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr14:56137400-56154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr14:56137400-56155000	Strong transcription	Adipose Nuclei	Adipose
18	chr14:56138600-56155200	Strong transcription	A549	lung
19	chr14:56141400-56154400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr14:56142800-56168400	Weak transcription	Fetal Kidney	kidney
21	chr14:56145600-56154000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr14:56145800-56154000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr14:56145800-56156800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr14:56145800-56157200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:56146400-56155600	Weak transcription	Spleen	Spleen
26	chr14:56146800-56156800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:56146800-56157800	Weak transcription	Fetal Brain Male	brain
28	chr14:56147000-56155200	Weak transcription	Fetal Brain Female	brain
29	chr14:56147400-56154600	Weak transcription	Brain Hippocampus Middle	brain
30	chr14:56147400-56170400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr14:56147600-56157200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr14:56147800-56156400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr14:56147800-56156800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr14:56147800-56164200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:56148000-56161800	Weak transcription	Pancreas	Pancrea
36	chr14:56148000-56174000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr14:56148200-56154200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr14:56148400-56165600	Weak transcription	NHDF-Ad	bronchial
39	chr14:56150600-56154000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr14:56150600-56155000	Strong transcription	GM12878-XiMat	blood
41	chr14:56150800-56154200	Weak transcription	Brain Substantia Nigra	brain
42	chr14:56150800-56157400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr14:56151000-56155600	Strong transcription	Primary T cells from cord blood	blood
44	chr14:56151200-56165800	Weak transcription	Hela-S3	cervix
45	chr14:56151400-56154000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr14:56151400-56154000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr14:56151400-56154000	Strong transcription	Lung	lung
48	chr14:56151400-56154200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr14:56151400-56154400	Strong transcription	Fetal Muscle Leg	muscle
50	chr14:56152000-56154000	Strong transcription	Aorta	Aorta

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