Variant report

Variant	rs9972178
Chromosome Location	chr14:56073480-56073481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:56072488..56077213-chr14:56077351..56081424,5	MCF-7	breast:
2	chr14:56050702..56052550-chr14:56072121..56074340,2	MCF-7	breast:
3	chr14:56045563..56049831-chr14:56070021..56074059,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126777	Chromatin interaction
ENSG00000186615	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10083303	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083353	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083431	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10083499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129890	0.85[AMR][1000 genomes]
rs10133729	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10133962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135124	1.00[YRI][hapmap]
rs10135426	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135600	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136155	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137364	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137885	0.88[EUR][1000 genomes]
rs10139905	0.88[EUR][1000 genomes]
rs10142497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142757	1.00[CEU][hapmap];1.00[CHB][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]
rs10142869	1.00[YRI][hapmap]
rs10143002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145687	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146604	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10147380	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147431	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148122	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148188	0.94[AFR][1000 genomes]
rs10148983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149408	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10150498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151664	0.82[AMR][1000 genomes]
rs10483643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483646	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs10483648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11546	1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12100949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs12323476	0.88[EUR][1000 genomes]
rs12879564	0.88[AMR][1000 genomes]
rs12879705	0.81[AMR][1000 genomes]
rs12880362	0.88[AMR][1000 genomes]
rs12883972	0.84[AMR][1000 genomes]
rs12886406	0.88[AMR][1000 genomes]
rs12892022	1.00[CHB][hapmap]
rs12893061	0.88[AMR][1000 genomes]
rs12893610	0.88[AMR][1000 genomes]
rs12893676	0.88[AMR][1000 genomes]
rs12894368	1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs12894613	0.88[AMR][1000 genomes]
rs13379151	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379264	0.94[AFR][1000 genomes]
rs13379340	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379343	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379353	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17253716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253730	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17253744	0.88[EUR][1000 genomes]
rs17683614	1.00[CHB][hapmap];0.92[AMR][1000 genomes]
rs17683626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes]
rs17683656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683728	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745274	0.81[AMR][1000 genomes]
rs17745459	1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs17746033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746106	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17832371	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147114	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28366673	0.94[AFR][1000 genomes]
rs28373835	0.94[AFR][1000 genomes]
rs28375514	0.84[EUR][1000 genomes]
rs28380739	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28392709	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409547	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478195	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513551	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537145	0.82[EUR][1000 genomes]
rs28539882	0.88[EUR][1000 genomes]
rs28549152	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581185	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587929	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616134	0.84[EUR][1000 genomes]
rs28656140	0.82[AFR][1000 genomes]
rs28661008	0.81[EUR][1000 genomes]
rs28663681	0.84[EUR][1000 genomes]
rs28681420	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754619	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831725	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34136598	0.88[AMR][1000 genomes]
rs34330219	0.88[AMR][1000 genomes]
rs34446601	0.88[AMR][1000 genomes]
rs34719936	0.88[AMR][1000 genomes]
rs35230683	0.88[AMR][1000 genomes]
rs35294669	0.88[AMR][1000 genomes]
rs35418987	0.88[AMR][1000 genomes]
rs35466279	0.88[AMR][1000 genomes]
rs35536987	0.88[AMR][1000 genomes]
rs35830444	0.88[AMR][1000 genomes]
rs3736876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742570	0.88[AMR][1000 genomes]
rs3742571	0.84[AMR][1000 genomes]
rs45458197	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45501402	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58569951	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58589065	0.88[EUR][1000 genomes]
rs71412688	0.88[AMR][1000 genomes]
rs71412689	0.88[AMR][1000 genomes]
rs71412690	0.88[AMR][1000 genomes]
rs71413577	0.88[AMR][1000 genomes]
rs71413578	0.88[AMR][1000 genomes]
rs7145064	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74051609	0.90[EUR][1000 genomes]
rs74053651	0.90[EUR][1000 genomes]
rs8006705	0.90[EUR][1000 genomes]
rs8007065	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009239	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009608	1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013714	0.90[EUR][1000 genomes]
rs8013831	0.90[EUR][1000 genomes]
rs8017891	0.90[EUR][1000 genomes]
rs8018142	0.90[EUR][1000 genomes]
rs8019218	0.84[AMR][1000 genomes]
rs9323289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972180	1.00[CEU][hapmap];1.00[CHB][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]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9972178	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:56052000-56080200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr14:56056200-56076000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr14:56061000-56085400	Weak transcription	Fetal Kidney	kidney
5	chr14:56061000-56085400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:56061200-56082400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr14:56064200-56082800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:56066400-56079000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:56066400-56079800	Weak transcription	K562	blood
10	chr14:56066600-56076200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:56066600-56079000	Weak transcription	Fetal Intestine Large	intestine
12	chr14:56066600-56079200	Weak transcription	Placenta	Placenta
13	chr14:56066600-56086200	Weak transcription	Fetal Intestine Small	intestine
14	chr14:56066600-56086200	Weak transcription	Gastric	stomach
15	chr14:56066800-56079200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr14:56066800-56080000	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:56066800-56086200	Weak transcription	Fetal Stomach	stomach
18	chr14:56067400-56074600	Enhancers	HepG2	liver
19	chr14:56067600-56080600	Weak transcription	GM12878-XiMat	blood
20	chr14:56067800-56075800	Weak transcription	NHLF	lung
21	chr14:56067800-56079000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr14:56067800-56082200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr14:56068000-56081400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr14:56068600-56074200	Weak transcription	HMEC	breast
25	chr14:56068600-56080400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr14:56068600-56086200	Weak transcription	Spleen	Spleen
27	chr14:56068600-56086600	Weak transcription	Lung	lung
28	chr14:56068800-56075800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:56068800-56075800	Weak transcription	Ovary	ovary
30	chr14:56068800-56080600	Weak transcription	Esophagus	oesophagus
31	chr14:56068800-56081000	Weak transcription	Liver	Liver
32	chr14:56069600-56075400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:56069600-56079000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr14:56069600-56086800	Weak transcription	Pancreas	Pancrea
35	chr14:56069800-56073800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr14:56069800-56074000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:56069800-56079200	Weak transcription	Primary T cells from cord blood	blood
38	chr14:56070000-56079000	Weak transcription	Primary B cells from cord blood	blood
39	chr14:56070400-56074000	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr14:56070400-56086200	Weak transcription	Aorta	Aorta
41	chr14:56070600-56075400	Weak transcription	Right Atrium	heart
42	chr14:56070600-56079000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr14:56070600-56079200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr14:56070800-56074200	Weak transcription	Small Intestine	intestine
45	chr14:56070800-56076000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr14:56070800-56079800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr14:56070800-56083000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr14:56070800-56085000	Weak transcription	Colon Smooth Muscle	Colon
49	chr14:56071000-56074200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr14:56071000-56074200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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