Variant report

Variant	rs16872190
Chromosome Location	chr6:12020289-12020290
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	chr6:12017880..12021749-chr6:12024798..12028599,4	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs17486782	1.00[ASN][1000 genomes]
rs17676319	1.00[ASN][1000 genomes]
rs2024579	1.00[ASN][1000 genomes]
rs41273100	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698720	1.00[ASN][1000 genomes]
rs55706944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55718735	1.00[ASN][1000 genomes]
rs55760539	1.00[ASN][1000 genomes]
rs55797398	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55819840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55839618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55875423	1.00[ASN][1000 genomes]
rs55911725	1.00[ASN][1000 genomes]
rs55964029	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56050214	1.00[ASN][1000 genomes]
rs56087670	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115353	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56204496	1.00[ASN][1000 genomes]
rs56209525	1.00[ASN][1000 genomes]
rs56294425	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321224	1.00[ASN][1000 genomes]
rs56412238	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56764416	1.00[ASN][1000 genomes]
rs57774273	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58026118	1.00[ASN][1000 genomes]
rs58086722	1.00[ASN][1000 genomes]
rs58221347	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58831065	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59206097	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59592071	1.00[ASN][1000 genomes]
rs60200272	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60552066	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61227873	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62395405	1.00[ASN][1000 genomes]
rs6458056	1.00[ASN][1000 genomes]
rs66530314	1.00[ASN][1000 genomes]
rs66614912	1.00[ASN][1000 genomes]
rs66708680	1.00[ASN][1000 genomes]
rs66720565	1.00[ASN][1000 genomes]
rs66727286	1.00[ASN][1000 genomes]
rs66964129	1.00[ASN][1000 genomes]
rs67170588	1.00[ASN][1000 genomes]
rs67757013	1.00[ASN][1000 genomes]
rs67843209	1.00[ASN][1000 genomes]
rs68009879	1.00[ASN][1000 genomes]
rs68019130	1.00[ASN][1000 genomes]
rs6916070	1.00[ASN][1000 genomes]
rs72826009	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826011	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826092	1.00[ASN][1000 genomes]
rs72828105	1.00[ASN][1000 genomes]
rs742750	1.00[ASN][1000 genomes]
rs876829	1.00[ASN][1000 genomes]

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	nsv970323	chr6:12006884-12020375	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3450161	chr6:12019874-12020378	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12013800-12033600	Weak transcription	Psoas Muscle	Psoas
2	chr6:12014000-12020400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:12014000-12023200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:12014000-12023200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:12014000-12031800	Weak transcription	Brain Substantia Nigra	brain
6	chr6:12014400-12023200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:12014400-12024800	Weak transcription	Stomach Mucosa	stomach
8	chr6:12014400-12030000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:12014600-12020400	Weak transcription	Fetal Heart	heart
10	chr6:12014600-12020600	Weak transcription	Right Atrium	heart
11	chr6:12014600-12021800	ZNF genes & repeats	GM12878-XiMat	blood
12	chr6:12014600-12032000	Weak transcription	Brain Angular Gyrus	brain
13	chr6:12015000-12021000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:12015000-12022000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:12015000-12022000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:12015000-12022000	Strong transcription	Fetal Muscle Leg	muscle
17	chr6:12015200-12021200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:12015200-12021400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:12015200-12021800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr6:12015200-12023400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:12015200-12024600	Weak transcription	NHDF-Ad	bronchial
22	chr6:12015400-12020400	Weak transcription	Aorta	Aorta
23	chr6:12015400-12021000	Strong transcription	NHLF	lung
24	chr6:12015400-12021400	Strong transcription	NHEK	skin
25	chr6:12015400-12023200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:12015400-12025000	Weak transcription	Small Intestine	intestine
27	chr6:12015400-12025400	Strong transcription	Liver	Liver
28	chr6:12015400-12029200	Weak transcription	Brain Anterior Caudate	brain
29	chr6:12015400-12034000	Weak transcription	Hela-S3	cervix
30	chr6:12015600-12022000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:12015600-12023000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:12016000-12021800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:12016000-12022000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:12016200-12020800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr6:12016200-12022000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:12016400-12020800	Strong transcription	Fetal Lung	lung
37	chr6:12016400-12022000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:12016800-12022000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:12017000-12020600	Strong transcription	Spleen	Spleen
40	chr6:12017000-12021000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:12017000-12021000	Strong transcription	Rectal Smooth Muscle	rectum
42	chr6:12017000-12021000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:12017000-12022400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:12017000-12023400	Strong transcription	Fetal Intestine Small	intestine
45	chr6:12017200-12020600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:12017200-12021800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr6:12017600-12020800	Strong transcription	Lung	lung
48	chr6:12017600-12022000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:12017800-12020400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:12017800-12020400	Weak transcription	Primary B cells from cord blood	blood

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