Variant report

Variant	rs9378943
Chromosome Location	chr6:5207603-5207604
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: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1055415	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12174086	0.95[ASN][1000 genomes]
rs12206736	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1535041	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1570085	0.83[ASN][1000 genomes]
rs1609808	0.85[ASN][1000 genomes]
rs17139748	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17139985	0.82[ASN][1000 genomes]
rs1884976	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1970010	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2145372	0.85[ASN][1000 genomes]
rs2224391	0.83[ASN][1000 genomes]
rs2224392	0.83[ASN][1000 genomes]
rs2746220	0.92[EUR][1000 genomes]
rs2746221	0.97[EUR][1000 genomes]
rs2746222	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2746224	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2746226	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2746243	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2753214	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2753222	0.83[ASN][1000 genomes]
rs2753223	0.85[ASN][1000 genomes]
rs2753224	0.85[ASN][1000 genomes]
rs2753228	0.85[ASN][1000 genomes]
rs2753229	0.85[ASN][1000 genomes]
rs2753230	0.85[ASN][1000 genomes]
rs2753233	0.83[ASN][1000 genomes]
rs2753234	0.83[ASN][1000 genomes]
rs2753235	0.82[ASN][1000 genomes]
rs2753237	0.83[ASN][1000 genomes]
rs2753238	0.82[ASN][1000 genomes]
rs2753239	0.83[ASN][1000 genomes]
rs2753240	0.83[ASN][1000 genomes]
rs2753243	0.81[ASN][1000 genomes]
rs2753244	0.83[ASN][1000 genomes]
rs2753245	0.83[ASN][1000 genomes]
rs2753246	0.82[ASN][1000 genomes]
rs2753247	0.82[ASN][1000 genomes]
rs2753248	0.82[ASN][1000 genomes]
rs2753249	0.82[ASN][1000 genomes]
rs2753255	0.84[EUR][1000 genomes]
rs2773287	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2773289	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2773291	0.87[EUR][1000 genomes]
rs2773294	0.84[EUR][1000 genomes]
rs2773296	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2773298	0.83[ASN][1000 genomes]
rs2773299	0.84[ASN][1000 genomes]
rs2773300	0.81[ASN][1000 genomes]
rs2773302	0.84[ASN][1000 genomes]
rs2773304	0.83[ASN][1000 genomes]
rs2773306	0.85[ASN][1000 genomes]
rs2773307	0.85[ASN][1000 genomes]
rs2773308	0.85[ASN][1000 genomes]
rs2773310	0.83[ASN][1000 genomes]
rs2773311	0.83[ASN][1000 genomes]
rs2773312	0.83[ASN][1000 genomes]
rs2773314	0.83[ASN][1000 genomes]
rs2773316	0.83[ASN][1000 genomes]
rs2773317	0.83[ASN][1000 genomes]
rs2773318	0.83[ASN][1000 genomes]
rs2773319	0.83[ASN][1000 genomes]
rs2773320	0.82[ASN][1000 genomes]
rs2773322	0.82[ASN][1000 genomes]
rs2773333	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2773335	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2773336	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2773337	0.93[EUR][1000 genomes]
rs2773339	0.93[EUR][1000 genomes]
rs35943326	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs367803	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs374253	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs391313	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs393391	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs393454	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs399283	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs409295	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs416803	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs419778	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs421186	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs421720	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4246073	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs429031	0.97[EUR][1000 genomes]
rs429490	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs434450	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs439356	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs445711	0.93[EUR][1000 genomes]
rs447604	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4960073	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4960074	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6909619	0.83[ASN][1000 genomes]
rs6913120	0.83[ASN][1000 genomes]
rs6925249	0.82[ASN][1000 genomes]
rs761359	0.93[EUR][1000 genomes]
rs761360	0.93[EUR][1000 genomes]
rs761361	0.93[EUR][1000 genomes]
rs766339	0.85[ASN][1000 genomes]
rs766340	0.85[ASN][1000 genomes]
rs7752203	0.83[ASN][1000 genomes]
rs928170	0.83[ASN][1000 genomes]
rs9328289	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378420	0.92[ASN][1000 genomes]
rs9392664	0.91[ASN][1000 genomes]
rs9392665	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9392666	0.83[ASN][1000 genomes]
rs9405259	0.98[ASN][1000 genomes]
rs9405260	0.90[ASN][1000 genomes]
rs9405807	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9405809	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9405811	0.82[ASN][1000 genomes]
rs9405813	0.88[ASN][1000 genomes]
rs9504356	0.83[EUR][1000 genomes]
rs9504364	0.83[ASN][1000 genomes]
rs9504365	0.83[ASN][1000 genomes]
rs9504369	0.82[ASN][1000 genomes]
rs9504371	0.82[ASN][1000 genomes]
rs9784870	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
15	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	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	chr6:5180200-5212200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:5180600-5208200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:5182000-5213600	Weak transcription	Gastric	stomach
5	chr6:5189000-5213200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:5192800-5213000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:5193200-5212400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:5194000-5220800	Weak transcription	GM12878-XiMat	blood
9	chr6:5195800-5207800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:5199800-5207800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:5201200-5208800	Enhancers	Fetal Muscle Leg	muscle
12	chr6:5201600-5213400	Weak transcription	Fetal Brain Male	brain
13	chr6:5201800-5213400	Weak transcription	Fetal Brain Female	brain
14	chr6:5202000-5212800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:5202800-5208400	Enhancers	Brain Anterior Caudate	brain
16	chr6:5202800-5213600	Weak transcription	Dnd41	blood
17	chr6:5203200-5210000	Enhancers	Fetal Stomach	stomach
18	chr6:5203400-5208600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:5203600-5210400	Enhancers	Colon Smooth Muscle	Colon
20	chr6:5203800-5208400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:5203800-5209000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:5203800-5213400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:5204000-5208600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:5204200-5208400	Enhancers	Brain Cingulate Gyrus	brain
25	chr6:5204200-5208600	Enhancers	Fetal Kidney	kidney
26	chr6:5204200-5209400	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:5204400-5208600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr6:5204400-5213000	Weak transcription	Hela-S3	cervix
29	chr6:5204600-5208800	Enhancers	Brain Angular Gyrus	brain
30	chr6:5204800-5208200	Enhancers	NHDF-Ad	bronchial
31	chr6:5204800-5208400	Enhancers	Liver	Liver
32	chr6:5204800-5208800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr6:5205200-5208600	Enhancers	Aorta	Aorta
34	chr6:5205400-5208000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:5205600-5208200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:5205600-5212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:5205600-5213000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:5205600-5213400	Weak transcription	Fetal Thymus	thymus
39	chr6:5205600-5218800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr6:5205600-5220000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:5205600-5223000	Weak transcription	Right Atrium	heart
42	chr6:5205800-5208600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:5206200-5214800	Weak transcription	Esophagus	oesophagus
44	chr6:5206200-5215600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr6:5206200-5215600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:5206200-5246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:5206400-5212600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:5206400-5213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:5206400-5214000	Weak transcription	Spleen	Spleen
50	chr6:5206400-5219400	Weak transcription	HMEC	breast

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