Variant report

Variant	rs7154889
Chromosome Location	chr14:55806885-55806886
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	NFIC	chr14:55806407-55806901	GM12878	blood:	n/a	n/a
2	RUNX3	chr14:55806368-55806896	GM12878	blood:	n/a	n/a
3	MEF2A	chr14:55806445-55806927	GM12878	blood:	n/a	n/a
4	RUNX3	chr14:55806391-55806900	GM12878	blood:	n/a	n/a
5	FOXM1	chr14:55806416-55806949	GM12878	blood:	n/a	n/a
6	MTA3	chr14:55806362-55806969	GM12878	blood:	n/a	n/a
7	BCLAF1	chr14:55806406-55806901	GM12878	blood:	n/a	n/a
8	MEF2A	chr14:55806457-55806916	GM12878	blood:	n/a	n/a
9	MEF2C	chr14:55806372-55806981	GM12878	blood:	n/a	chr14:55806402-55806417
10	ATF2	chr14:55806392-55806963	GM12878	blood:	n/a	n/a
11	NFATC1	chr14:55806348-55806972	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55738126..55740346-chr14:55806571..55808200,2	MCF-7	breast:
2	chr14:55736427..55740242-chr14:55801434..55807681,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258455	TF binding region
ENSG00000258413	Chromatin interaction
ENSG00000178974	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10129505	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10131562	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10131730	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10131913	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10131926	0.83[AFR][1000 genomes]
rs10134317	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10134339	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10136596	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs10137307	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]
rs10139000	0.96[EUR][1000 genomes]
rs10139083	0.82[EUR][1000 genomes]
rs10140801	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs10140869	0.93[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs10141396	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10141483	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10141552	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10142448	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs10142547	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10142823	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10144345	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10144418	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10145203	0.84[EUR][1000 genomes]
rs10146637	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10147765	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10149420	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10150699	0.81[EUR][1000 genomes]
rs10150760	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1045002	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1045004	0.81[JPT][hapmap]
rs10467798	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1109170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11158034	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs11547116	0.80[EUR][1000 genomes]
rs11621265	0.81[JPT][hapmap]
rs11622740	0.82[CEU][hapmap]
rs11625001	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11625423	0.85[EUR][1000 genomes]
rs11625968	0.96[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]
rs11626751	0.94[EUR][1000 genomes]
rs11628437	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11851169	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13379169	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1572611	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs17128440	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17674463	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17674563	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17740741	0.93[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs17741542	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17741831	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1815580	0.92[EUR][1000 genomes]
rs1815581	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1952087	0.85[AFR][1000 genomes]
rs1972221	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2009291	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2016931	0.96[EUR][1000 genomes]
rs2026633	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2075601	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2075602	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2075603	0.82[CEU][hapmap]
rs2182797	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209808	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274273	0.81[CEU][hapmap]
rs2340931	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs2341621	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2341622	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28428911	0.96[EUR][1000 genomes]
rs28430823	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28493647	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28568813	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28612464	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28631821	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28660594	0.96[EUR][1000 genomes]
rs28716725	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2880103	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3742569	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3783648	0.92[EUR][1000 genomes]
rs3783650	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3783651	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3783652	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs3818451	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs3825616	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4366639	0.85[EUR][1000 genomes]
rs4496026	0.85[EUR][1000 genomes]
rs4597235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56270323	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56949365	0.84[EUR][1000 genomes]
rs58260073	0.81[EUR][1000 genomes]
rs59629906	0.81[EUR][1000 genomes]
rs59871474	0.81[EUR][1000 genomes]
rs61210954	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6573009	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6573010	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6573013	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6573014	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6573017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573020	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66486619	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66696758	0.81[EUR][1000 genomes]
rs67514154	0.80[EUR][1000 genomes]
rs7142857	0.81[AFR][1000 genomes]
rs7144737	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7145727	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7146748	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7146752	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7147136	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7147247	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7148171	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7150234	0.82[ASN][1000 genomes]
rs7150763	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7151581	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7152390	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7153110	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7153612	0.84[EUR][1000 genomes]
rs7153645	0.81[EUR][1000 genomes]
rs7155954	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7158768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7158791	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7159144	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7159808	0.93[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs7159824	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs8004787	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs8005450	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs8006525	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8008119	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8013027	0.86[CEU][hapmap]
rs8013713	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8014477	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs8014540	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs8015211	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs8018110	0.85[AFR][1000 genomes]
rs8021583	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs8022041	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8022225	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8023197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9323284	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9323285	0.81[JPT][hapmap]
rs943590	0.82[EUR][1000 genomes]
rs946059	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9919926	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs9919932	0.82[CHB][hapmap];0.86[JPT][hapmap]

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	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv84773	chr14:55804786-55807119	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7154889	RP11-665C16.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55779200-55817600	Weak transcription	Hela-S3	cervix
2	chr14:55780200-55807800	Weak transcription	Thymus	Thymus
3	chr14:55780800-55817200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr14:55782000-55817200	Weak transcription	HSMM	muscle
5	chr14:55791800-55817200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:55793000-55808600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr14:55794000-55811800	Weak transcription	Brain Anterior Caudate	brain
8	chr14:55797800-55807800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr14:55798200-55817200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr14:55800000-55817200	Weak transcription	Dnd41	blood
11	chr14:55800600-55816200	Weak transcription	Primary B cells from cord blood	blood
12	chr14:55800600-55823600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr14:55801000-55807800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr14:55801000-55808400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr14:55801000-55808600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr14:55801000-55817200	Weak transcription	HepG2	liver
17	chr14:55801200-55817200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:55801200-55817200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr14:55801200-55817200	Weak transcription	Liver	Liver
20	chr14:55801200-55817200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr14:55801200-55842800	Weak transcription	Fetal Brain Male	brain
22	chr14:55801400-55817400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr14:55801400-55817400	Weak transcription	Brain Hippocampus Middle	brain
24	chr14:55801600-55807000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr14:55801600-55807200	Enhancers	Primary T cells from cord blood	blood
26	chr14:55801600-55817200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr14:55801800-55807000	Weak transcription	Right Atrium	heart
28	chr14:55802000-55807200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr14:55802200-55817000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:55802200-55817400	Weak transcription	Fetal Intestine Small	intestine
31	chr14:55802800-55808000	Enhancers	Primary T cells fromperipheralblood	blood
32	chr14:55803000-55808000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr14:55803200-55808000	Weak transcription	Osteobl	bone
34	chr14:55803200-55808200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr14:55803200-55809000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr14:55803400-55809200	Weak transcription	Colonic Mucosa	Colon
37	chr14:55803400-55817200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr14:55803400-55817200	Weak transcription	Placenta	Placenta
39	chr14:55803600-55817200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr14:55804400-55807600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr14:55804400-55811000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr14:55804600-55808800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr14:55804800-55807000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr14:55804800-55811400	Weak transcription	Gastric	stomach
45	chr14:55805000-55807000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr14:55805200-55811800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr14:55805200-55813600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr14:55805200-55817200	Weak transcription	Fetal Intestine Large	intestine
49	chr14:55805400-55808200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr14:55805400-55810400	Weak transcription	Stomach Mucosa	stomach

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