Variant report

Variant	rs3742881
Chromosome Location	chr14:68159626-68159627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:68159284-68159964	K562	blood:	n/a	n/a
2	STAT3	chr14:68159513-68159713	MCF10A-Er-Src	breast:	n/a	chr14:68159583-68159592 chr14:68159582-68159591
3	FOS	chr14:68159408-68159755	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr14:68159593-68160103	HepG2	liver:	n/a	n/a
5	FOS	chr14:68159418-68159760	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr14:68159492-68159681	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:68159603..68161982-chr14:68281864..68284626,4	MCF-7	breast:
2	chr14:68139847..68143415-chr14:68157981..68164641,9	K562	blood:
3	chr14:68139320..68145896-chr14:68154797..68164104,19	MCF-7	breast:
4	chr14:68139933..68142840-chr14:68159503..68163270,4	K562	blood:
5	chr14:68138842..68143559-chr14:68155519..68164066,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258466	TF binding region
RDH11	TF binding region
ENSG00000072121	Chromatin interaction
ENSG00000100568	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10459532	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059238	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1120877	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11620761	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11622441	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11623700	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11623711	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11623785	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11623961	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11624498	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11624868	0.88[EUR][1000 genomes]
rs11625839	0.93[EUR][1000 genomes]
rs11627201	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11628860	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12050393	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1555193	0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17104490	0.82[ASW][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17104526	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17104544	0.82[ASW][hapmap];0.92[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17104550	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17104597	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17104621	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17249472	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17852293	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955472	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1955473	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2234511	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2320029	0.84[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28390085	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28532066	0.84[EUR][1000 genomes]
rs28873201	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3742880	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4899221	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4899222	1.00[ASW][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4902506	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4902511	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902512	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55900323	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56244142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56256221	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60581344	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6573790	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs6573794	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6573795	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7140310	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs7142897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144076	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144124	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144186	0.86[EUR][1000 genomes]
rs7151205	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7151230	0.85[EUR][1000 genomes]
rs7152326	0.84[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7155788	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7159889	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72721082	0.88[EUR][1000 genomes]
rs72721090	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72723111	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723115	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723122	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72723126	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72723137	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72723144	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723150	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72723152	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72723154	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72723155	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72723156	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72723158	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72723160	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72723163	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72723166	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72723167	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs742865	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs761513	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761514	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8009250	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8013767	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8017147	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8017326	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8019831	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8020591	0.91[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][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	nsv902068	chr14:68083133-68204876	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
2	nsv1042536	chr14:68136913-68343198	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv542122	chr14:68136913-68343198	Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv521832	chr14:68141009-68204876	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3742881	RDH11	Cis_1M	lymphoblastoid	RTeQTL
rs3742881	ATP6V1D	cis	parietal	SCAN
rs3742881	ZBTB1	cis	cerebellum	SCAN
rs3742881	RDH11	cis	Nerve Tibial	GTEx
rs3742881	C14orf162	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68142400-68160600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:68142400-68160800	Weak transcription	Right Atrium	heart
3	chr14:68143000-68160200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr14:68143200-68160600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr14:68143400-68160800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr14:68143800-68159800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr14:68143800-68160000	Strong transcription	Fetal Thymus	thymus
8	chr14:68143800-68160200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr14:68144200-68159800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr14:68144200-68160000	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr14:68144200-68160000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:68144200-68160000	Strong transcription	Primary T cells from cord blood	blood
13	chr14:68144200-68160200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr14:68144200-68160400	Strong transcription	Fetal Muscle Leg	muscle
15	chr14:68144200-68160800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr14:68144600-68160600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:68144800-68159800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:68144800-68159800	Strong transcription	Liver	Liver
19	chr14:68147600-68160200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr14:68148000-68159800	Strong transcription	A549	lung
21	chr14:68148000-68160000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr14:68148200-68159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr14:68148200-68159800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr14:68148400-68160000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr14:68148600-68159800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr14:68148600-68159800	Strong transcription	HSMM	muscle
27	chr14:68149000-68159800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr14:68149000-68160000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr14:68149200-68159800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr14:68149200-68160000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr14:68149600-68159800	Strong transcription	HSMMtube	muscle
32	chr14:68150400-68159800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:68150400-68159800	Strong transcription	Fetal Stomach	stomach
34	chr14:68150800-68160800	Weak transcription	Fetal Heart	heart
35	chr14:68151000-68159800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr14:68151800-68159800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr14:68151800-68159800	Strong transcription	Thymus	Thymus
38	chr14:68151800-68159800	Strong transcription	Hela-S3	cervix
39	chr14:68151800-68160000	Strong transcription	Fetal Brain Female	brain
40	chr14:68152800-68160000	Strong transcription	Brain Substantia Nigra	brain
41	chr14:68153000-68161600	Weak transcription	Psoas Muscle	Psoas
42	chr14:68153600-68160200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr14:68155400-68159800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr14:68155600-68159800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr14:68155600-68160000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:68156000-68160800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr14:68157400-68161400	Weak transcription	Stomach Mucosa	stomach
48	chr14:68157600-68161400	Weak transcription	Right Ventricle	heart
49	chr14:68157800-68160200	Weak transcription	Fetal Brain Male	brain
50	chr14:68158000-68160400	Weak transcription	Esophagus	oesophagus

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