Variant report

Variant	rs17841064
Chromosome Location	chr14:103900609-103900610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:103900219..103903734-chr14:103907448..103910788,3	K562	blood:
2	chr14:103869618..103871185-chr14:103898241..103901206,2	MCF-7	breast:
3	chr14:103894939..103897100-chr14:103899753..103901391,2	MCF-7	breast:
4	chr14:103887007..103890737-chr14:103900205..103902802,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075413	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10144051	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10148970	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10149470	0.88[JPT][hapmap]
rs10151483	0.82[EUR][1000 genomes]
rs10162425	1.00[CEU][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1107070	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11160751	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1116095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1138400	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11620897	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11627446	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12431617	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12432803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12435516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12436729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12436759	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12436956	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12588272	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12878548	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12882393	0.83[ASN][1000 genomes]
rs12894652	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17101620	0.85[ASN][1000 genomes]
rs2023395	0.85[EUR][1000 genomes]
rs2071407	0.83[ASW][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs2273701	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273702	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2403174	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2403192	0.85[EUR][1000 genomes]
rs2756122	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2756128	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2756132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2756135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2765046	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2765049	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2765051	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34251103	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34411783	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34831235	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35233301	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35374941	0.83[ASN][1000 genomes]
rs35410438	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35512556	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759575	0.85[ASN][1000 genomes]
rs3759577	0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs3783399	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4143998	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4243738	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4243739	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4900573	0.83[ASN][1000 genomes]
rs4900580	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4906319	0.83[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs4906320	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4906322	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4906324	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55658071	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55742283	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57344120	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60235428	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6575982	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6575983	0.83[YRI][hapmap]
rs6575985	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6575986	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6575988	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6575991	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140647	0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144010	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7144271	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7145753	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7146215	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7147640	0.86[AMR][1000 genomes]
rs7147664	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7148567	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7148614	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7149767	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7156036	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7156471	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7159668	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7160888	0.83[ASN][1000 genomes]
rs8003740	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8010247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8014013	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];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8014800	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8015429	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8015712	0.81[ASN][1000 genomes]
rs8016676	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8018400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8020912	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs911552	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs911554	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs911555	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9671414	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs975892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription 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 target site	125 gene(s)	inside rSNPs	diseases
3	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17841064	KLC1	cis	parietal	SCAN
rs17841064	MARK3	cis	multi-tissue	Pritchard
rs17841064	NCRNA00221	cis	cerebellum	SCAN
rs17841064	C14orf172	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103862000-103919400	Weak transcription	Colonic Mucosa	Colon
2	chr14:103874600-103900800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:103879000-103914200	Weak transcription	Esophagus	oesophagus
4	chr14:103879000-103941400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:103880400-103904600	Weak transcription	Fetal Kidney	kidney
6	chr14:103889400-103917800	Weak transcription	Gastric	stomach
7	chr14:103890000-103922400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:103890200-103905600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:103890200-103914200	Weak transcription	Lung	lung
10	chr14:103891000-103904000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr14:103893000-103904600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr14:103893200-103905600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:103894400-103911400	Weak transcription	Pancreas	Pancrea
14	chr14:103894400-103911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr14:103894600-103901400	Weak transcription	A549	lung
16	chr14:103894600-103904800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:103894600-103908200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:103894600-103911400	Weak transcription	Brain Angular Gyrus	brain
19	chr14:103894600-103911600	Weak transcription	Fetal Brain Female	brain
20	chr14:103894600-103922400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr14:103894600-103927400	Weak transcription	Hela-S3	cervix
22	chr14:103895400-103905400	Weak transcription	Fetal Lung	lung
23	chr14:103895600-103905000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:103895600-103905000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr14:103895600-103911400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr14:103895800-103901400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:103895800-103901400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr14:103895800-103904000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr14:103895800-103911200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr14:103895800-103911200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr14:103895800-103917800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr14:103896000-103901200	Weak transcription	Right Ventricle	heart
33	chr14:103896000-103902400	Weak transcription	Adipose Nuclei	Adipose
34	chr14:103896000-103906000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr14:103896000-103909800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr14:103896000-103911200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr14:103896000-103911400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr14:103896000-103911400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr14:103896000-103911400	Weak transcription	Ovary	ovary
40	chr14:103896000-103916600	Weak transcription	Small Intestine	intestine
41	chr14:103896000-103922400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:103896000-103922600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr14:103896200-103901200	Weak transcription	Fetal Heart	heart
44	chr14:103896200-103909800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr14:103896200-103911400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr14:103896400-103917800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr14:103896600-103901600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr14:103896800-103901600	Strong transcription	Primary T cells from cord blood	blood
49	chr14:103897200-103901400	Strong transcription	Fetal Intestine Small	intestine
50	chr14:103897400-103911200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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