Variant report

Variant	rs6977828
Chromosome Location	chr7:137559690-137559691
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:137555025..137557562-chr7:137558269..137560662,2	MCF-7	breast:
2	chr7:137550548..137553249-chr7:137557181..137559857,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10243295	1.00[TSI][hapmap]
rs10250405	0.87[ASN][1000 genomes]
rs10261211	1.00[TSI][hapmap]
rs10954590	1.00[GIH][hapmap]
rs11975719	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12673967	1.00[AMR][1000 genomes]
rs17169441	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1871214	1.00[TSI][hapmap]
rs3735016	0.87[ASN][1000 genomes]
rs3735019	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3735020	0.93[CHB][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs61640672	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6467716	1.00[TSI][hapmap]
rs6467721	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6943538	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs6958842	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6959012	0.94[CHB][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs6960308	1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6960313	0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs6971738	0.80[ASN][1000 genomes]
rs6976638	0.86[ASN][1000 genomes]
rs6976928	0.94[CHB][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs6980335	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs769037	0.83[ASN][1000 genomes]
rs769038	0.80[ASN][1000 genomes]
rs7788967	0.91[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs881505	1.00[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022793	chr7:137187383-137619359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv831150	chr7:137500559-137652808	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv518070	chr7:137534627-137808839	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137533800-137575400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:137534200-137563000	Weak transcription	HMEC	breast
3	chr7:137535200-137562600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr7:137543400-137566800	Strong transcription	Placenta	Placenta
5	chr7:137545000-137564200	Weak transcription	Small Intestine	intestine
6	chr7:137546200-137560000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:137546400-137562600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:137546400-137564000	Weak transcription	Brain Angular Gyrus	brain
9	chr7:137547200-137562200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:137547400-137561400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:137547800-137567200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:137548000-137562000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:137548400-137563200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:137549200-137560000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:137550200-137564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:137550600-137563400	Weak transcription	Brain Substantia Nigra	brain
17	chr7:137550800-137561200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:137550800-137562600	Weak transcription	Brain Anterior Caudate	brain
19	chr7:137551200-137569400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr7:137551400-137562600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr7:137551600-137560400	Weak transcription	K562	blood
22	chr7:137551600-137561400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:137551600-137562800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:137552800-137561400	Weak transcription	NHEK	skin
25	chr7:137553000-137560000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:137553000-137562600	Weak transcription	Primary T cells from cord blood	blood
27	chr7:137553000-137563200	Weak transcription	Colonic Mucosa	Colon
28	chr7:137555400-137561400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:137555600-137563800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:137555600-137583200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr7:137556000-137561400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:137556000-137561800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:137556000-137562000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:137556000-137563200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:137556000-137566800	Strong transcription	GM12878-XiMat	blood
36	chr7:137556000-137570800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr7:137556000-137573600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:137556400-137561000	Weak transcription	Fetal Brain Male	brain
39	chr7:137556400-137562800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:137556400-137564800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:137556600-137562800	Weak transcription	Gastric	stomach
42	chr7:137556600-137563200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:137557000-137561600	Strong transcription	Primary B cells from cord blood	blood
44	chr7:137557000-137566800	Strong transcription	Fetal Intestine Large	intestine
45	chr7:137557000-137570600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr7:137557200-137561800	Strong transcription	Brain Hippocampus Middle	brain
47	chr7:137557200-137564000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:137557200-137566800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr7:137557400-137560000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr7:137557400-137567200	Genic enhancers	Osteobl	bone

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