Variant report

Variant	rs6921061
Chromosome Location	chr6:5206044-5206045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5203877..5206736-chr6:5207600..5210343,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10498666	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17139873	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17140092	0.83[GIH][hapmap]
rs17312134	0.83[LWK][hapmap]
rs444607	0.96[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4481464	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55960383	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6921237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6939454	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73363048	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73363050	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73363073	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73363074	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73363091	0.88[EUR][1000 genomes]
rs73363098	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73365003	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7754129	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7766566	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7768590	0.88[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7771066	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7772716	1.00[ASW][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5176200-5239600	Weak transcription	Thymus	Thymus
2	chr6:5179200-5207600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:5180200-5212200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:5180600-5208200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:5182000-5213600	Weak transcription	Gastric	stomach
6	chr6:5189000-5213200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:5191000-5206600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:5191800-5206400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:5192800-5213000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:5193200-5212400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:5194000-5220800	Weak transcription	GM12878-XiMat	blood
12	chr6:5195800-5207800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:5199800-5206200	Enhancers	Fetal Heart	heart
14	chr6:5199800-5207800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:5200200-5206200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:5201200-5208800	Enhancers	Fetal Muscle Leg	muscle
17	chr6:5201600-5213400	Weak transcription	Fetal Brain Male	brain
18	chr6:5201800-5213400	Weak transcription	Fetal Brain Female	brain
19	chr6:5202000-5212800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:5202200-5206200	Enhancers	Brain Substantia Nigra	brain
21	chr6:5202400-5206200	Enhancers	NHEK	skin
22	chr6:5202400-5206400	Enhancers	HMEC	breast
23	chr6:5202400-5206600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:5202600-5206600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:5202600-5206800	Enhancers	Placenta	Placenta
26	chr6:5202800-5208400	Enhancers	Brain Anterior Caudate	brain
27	chr6:5202800-5213600	Weak transcription	Dnd41	blood
28	chr6:5203200-5210000	Enhancers	Fetal Stomach	stomach
29	chr6:5203400-5206600	Enhancers	Fetal Lung	lung
30	chr6:5203400-5208600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:5203600-5207400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:5203600-5207600	Enhancers	Brain Hippocampus Middle	brain
33	chr6:5203600-5210400	Enhancers	Colon Smooth Muscle	Colon
34	chr6:5203800-5206600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr6:5203800-5207200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:5203800-5207400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:5203800-5208400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:5203800-5209000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:5203800-5213400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:5204000-5206600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:5204000-5206800	Enhancers	Ovary	ovary
42	chr6:5204000-5206800	Enhancers	HUVEC	blood vessel
43	chr6:5204000-5207000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:5204000-5208600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:5204200-5206800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:5204200-5206800	Enhancers	Left Ventricle	heart
47	chr6:5204200-5207000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr6:5204200-5208400	Enhancers	Brain Cingulate Gyrus	brain
49	chr6:5204200-5208600	Enhancers	Fetal Kidney	kidney
50	chr6:5204200-5209400	Enhancers	Rectal Smooth Muscle	rectum

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