Variant report

Variant	rs1336242
Chromosome Location	chr6:101199634-101199635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101169269..101170858-chr6:101198475..101201217,2	MCF-7	breast:

Extended variants
information (count: 206 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:194)

rs_ID	r²[population]
rs10223467	0.87[EUR][1000 genomes]
rs1039030	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1039031	0.88[EUR][1000 genomes]
rs1039032	0.88[EUR][1000 genomes]
rs10457077	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10457844	0.92[EUR][1000 genomes]
rs10457849	0.88[EUR][1000 genomes]
rs1070990	0.87[EUR][1000 genomes]
rs10872622	0.88[EUR][1000 genomes]
rs10872628	0.92[EUR][1000 genomes]
rs10872634	0.91[EUR][1000 genomes]
rs1099916	0.89[EUR][1000 genomes]
rs11155596	0.82[EUR][1000 genomes]
rs11155606	0.82[EUR][1000 genomes]
rs11155610	0.82[EUR][1000 genomes]
rs11155613	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155618	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11155623	0.90[EUR][1000 genomes]
rs11155635	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11155636	0.92[EUR][1000 genomes]
rs11155637	0.92[EUR][1000 genomes]
rs11155638	0.92[EUR][1000 genomes]
rs11155653	0.91[EUR][1000 genomes]
rs11155659	0.91[EUR][1000 genomes]
rs11155666	0.91[EUR][1000 genomes]
rs11155673	0.87[EUR][1000 genomes]
rs11752659	0.90[EUR][1000 genomes]
rs11967951	0.92[EUR][1000 genomes]
rs12174806	0.87[EUR][1000 genomes]
rs12175456	0.84[EUR][1000 genomes]
rs12193960	0.82[EUR][1000 genomes]
rs12194255	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12195369	0.92[EUR][1000 genomes]
rs12199888	0.82[EUR][1000 genomes]
rs12201852	0.81[EUR][1000 genomes]
rs12202621	0.87[EUR][1000 genomes]
rs12206838	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12207086	0.82[EUR][1000 genomes]
rs12209777	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209887	0.88[EUR][1000 genomes]
rs12210255	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12210550	0.90[EUR][1000 genomes]
rs12212435	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212736	0.82[EUR][1000 genomes]
rs12213201	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12214151	0.82[EUR][1000 genomes]
rs12215909	0.96[EUR][1000 genomes]
rs12216199	0.82[EUR][1000 genomes]
rs12216304	0.84[EUR][1000 genomes]
rs12528607	0.90[EUR][1000 genomes]
rs12664626	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13196803	0.92[EUR][1000 genomes]
rs13208757	0.92[EUR][1000 genomes]
rs1336244	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336245	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1414734	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151572	0.81[EUR][1000 genomes]
rs151637	0.81[EUR][1000 genomes]
rs151638	0.86[EUR][1000 genomes]
rs151640	0.86[EUR][1000 genomes]
rs180963	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs183566	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2036052	0.82[EUR][1000 genomes]
rs2050549	0.87[EUR][1000 genomes]
rs2132168	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2132169	0.92[EUR][1000 genomes]
rs239189	0.81[EUR][1000 genomes]
rs239196	0.94[ASN][1000 genomes]
rs239197	0.81[EUR][1000 genomes]
rs239198	0.95[ASN][1000 genomes]
rs239201	0.81[EUR][1000 genomes]
rs239203	0.81[EUR][1000 genomes]
rs239204	0.81[EUR][1000 genomes]
rs239206	0.81[EUR][1000 genomes]
rs239207	0.80[EUR][1000 genomes]
rs239208	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239209	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239211	0.81[EUR][1000 genomes]
rs239215	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239216	0.82[EUR][1000 genomes]
rs239217	0.82[EUR][1000 genomes]
rs239218	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239219	0.81[EUR][1000 genomes]
rs239221	0.81[EUR][1000 genomes]
rs239222	0.81[EUR][1000 genomes]
rs239223	0.81[EUR][1000 genomes]
rs239226	0.81[EUR][1000 genomes]
rs239227	0.81[EUR][1000 genomes]
rs239229	0.81[EUR][1000 genomes]
rs239230	0.81[EUR][1000 genomes]
rs239231	0.81[EUR][1000 genomes]
rs239232	0.81[EUR][1000 genomes]
rs239234	0.86[EUR][1000 genomes]
rs239235	0.80[EUR][1000 genomes]
rs239236	0.86[EUR][1000 genomes]
rs240111	0.83[EUR][1000 genomes]
rs240149	0.82[EUR][1000 genomes]
rs240151	0.83[EUR][1000 genomes]
rs240152	0.83[EUR][1000 genomes]
rs34759265	0.81[EUR][1000 genomes]
rs35168784	0.91[EUR][1000 genomes]
rs35967345	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3811078	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs41288423	0.88[EUR][1000 genomes]
rs4463266	0.87[EUR][1000 genomes]
rs4571568	0.91[EUR][1000 genomes]
rs4839789	0.87[EUR][1000 genomes]
rs4839792	0.85[EUR][1000 genomes]
rs4840147	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840148	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840150	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840151	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840153	0.92[EUR][1000 genomes]
rs4840154	0.87[EUR][1000 genomes]
rs4840155	0.85[EUR][1000 genomes]
rs4840159	0.84[CEU][hapmap]
rs58266877	0.82[EUR][1000 genomes]
rs62422070	0.90[EUR][1000 genomes]
rs6570922	0.92[EUR][1000 genomes]
rs6570930	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570970	0.92[EUR][1000 genomes]
rs6903665	0.94[ASN][1000 genomes]
rs6904959	0.86[EUR][1000 genomes]
rs6905113	0.87[EUR][1000 genomes]
rs6905221	0.82[EUR][1000 genomes]
rs6907240	0.82[EUR][1000 genomes]
rs6907444	0.88[EUR][1000 genomes]
rs6909880	0.92[EUR][1000 genomes]
rs6916468	0.88[EUR][1000 genomes]
rs6919283	0.92[EUR][1000 genomes]
rs6919745	0.81[CEU][hapmap]
rs6922219	0.82[EUR][1000 genomes]
rs6925065	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925316	0.87[EUR][1000 genomes]
rs6925823	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6925840	0.91[EUR][1000 genomes]
rs6927598	0.92[EUR][1000 genomes]
rs6928418	0.92[ASN][1000 genomes]
rs6932158	0.86[EUR][1000 genomes]
rs6938440	0.82[EUR][1000 genomes]
rs705583	0.87[EUR][1000 genomes]
rs705584	0.87[EUR][1000 genomes]
rs705585	0.87[EUR][1000 genomes]
rs705586	0.89[EUR][1000 genomes]
rs723742	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs723743	0.92[EUR][1000 genomes]
rs7451736	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740783	0.84[EUR][1000 genomes]
rs7742011	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746947	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7746961	0.87[EUR][1000 genomes]
rs7747014	0.92[EUR][1000 genomes]
rs7748644	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754085	0.85[EUR][1000 genomes]
rs7768210	0.84[EUR][1000 genomes]
rs7771570	0.84[CEU][hapmap]
rs846778	0.82[EUR][1000 genomes]
rs846799	0.82[EUR][1000 genomes]
rs846800	0.87[EUR][1000 genomes]
rs846803	0.87[EUR][1000 genomes]
rs9322173	0.93[EUR][1000 genomes]
rs9322174	0.88[EUR][1000 genomes]
rs9322181	0.87[EUR][1000 genomes]
rs9322182	0.87[EUR][1000 genomes]
rs9322183	0.87[EUR][1000 genomes]
rs9322212	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9322213	0.86[EUR][1000 genomes]
rs9322216	0.91[EUR][1000 genomes]
rs9373590	0.92[EUR][1000 genomes]
rs9377214	0.87[EUR][1000 genomes]
rs9377234	0.89[EUR][1000 genomes]
rs9377235	0.89[EUR][1000 genomes]
rs9386233	0.94[ASN][1000 genomes]
rs9386250	0.87[EUR][1000 genomes]
rs9386257	0.86[EUR][1000 genomes]
rs9386259	0.86[YRI][hapmap]
rs9390679	0.87[EUR][1000 genomes]
rs9390681	0.85[EUR][1000 genomes]
rs9390685	0.87[EUR][1000 genomes]
rs9390693	0.92[EUR][1000 genomes]
rs9399685	0.87[EUR][1000 genomes]
rs9399688	0.91[EUR][1000 genomes]
rs9399694	0.85[EUR][1000 genomes]
rs9403997	0.94[ASN][1000 genomes]
rs9404016	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404045	0.92[EUR][1000 genomes]
rs9404049	0.87[EUR][1000 genomes]
rs9404052	0.86[EUR][1000 genomes]
rs9404053	0.85[EUR][1000 genomes]
rs9404054	0.85[EUR][1000 genomes]
rs9485410	0.85[EUR][1000 genomes]
rs9498252	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9498390	0.86[EUR][1000 genomes]
rs9498414	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv886445	chr6:101004751-101240763	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv886453	chr6:101018032-101203051	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886455	chr6:101049108-101203051	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv886456	chr6:101049108-101277926	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv604275	chr6:101158950-101277926	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv1016353	chr6:101172705-101304041	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv1024526	chr6:101192726-101241291	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101166200-101211000	Weak transcription	NH-A	brain
2	chr6:101168600-101211200	Weak transcription	Osteobl	bone
3	chr6:101169000-101211000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:101172800-101210800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:101173000-101209000	Weak transcription	K562	blood
6	chr6:101173000-101211000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:101175800-101211200	Weak transcription	Psoas Muscle	Psoas
8	chr6:101177000-101211600	Weak transcription	NHDF-Ad	bronchial
9	chr6:101182200-101214400	Weak transcription	A549	lung
10	chr6:101184400-101304600	Weak transcription	Hela-S3	cervix
11	chr6:101185400-101212600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:101186600-101208400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:101188400-101211400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:101189200-101209200	Weak transcription	Right Ventricle	heart
15	chr6:101190200-101211200	Weak transcription	Fetal Lung	lung
16	chr6:101190200-101211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:101190400-101205000	Weak transcription	Left Ventricle	heart
18	chr6:101190600-101206400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:101190600-101212600	Weak transcription	HSMMtube	muscle
20	chr6:101190800-101211000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:101190800-101216200	Weak transcription	Stomach Mucosa	stomach
22	chr6:101190800-101217400	Weak transcription	NHLF	lung
23	chr6:101191000-101208200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:101191000-101209000	Weak transcription	Lung	lung
25	chr6:101191000-101211200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:101191000-101211400	Weak transcription	Fetal Thymus	thymus
27	chr6:101191200-101202400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:101191200-101206400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:101191200-101207200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr6:101191200-101207200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:101191200-101207800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:101191200-101208200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:101191200-101209200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:101191200-101209200	Weak transcription	Fetal Stomach	stomach
35	chr6:101191200-101209800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:101191200-101211200	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:101191200-101211400	Weak transcription	Adipose Nuclei	Adipose
38	chr6:101191200-101211600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr6:101191200-101211600	Weak transcription	HepG2	liver
40	chr6:101191200-101211800	Weak transcription	Placenta	Placenta
41	chr6:101191400-101200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:101191400-101201200	Weak transcription	GM12878-XiMat	blood
43	chr6:101191400-101202000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:101191400-101202000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:101191400-101202200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:101191400-101202600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:101191400-101205800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:101191400-101206000	Weak transcription	Primary T cells from cord blood	blood
49	chr6:101191400-101206200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:101191400-101207800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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