Variant report

Variant	rs240364
Chromosome Location	chr6:75913720-75913721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:75913509-75913870	T-47D	breast:	n/a	n/a
2	CHD2	chr6:75913504-75914283	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr6:75913466-75914332	Hela-S3	cervix:	n/a	n/a
4	SMC3	chr6:75913424-75916272	Hela-S3	cervix:	n/a	n/a
5	GTF2F1	chr6:75913574-75914305	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr6:75913538-75917088	IMR90	lung:	n/a	chr6:75914516-75914523
7	SMARCC1	chr6:75913598-75916305	Hela-S3	cervix:	n/a	n/a
8	FOS	chr6:75913682-75914311	MCF10A-Er-Src	breast:	n/a	chr6:75914158-75914169
9	GATA3	chr6:75913453-75913924	T-47D	breast:	n/a	n/a
10	TCF7L2	chr6:75913564-75916132	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:75913472-75916719	IMR90	lung:	n/a	n/a
12	RAD21	chr6:75913447-75914499	SK-N-SH	brain:	n/a	n/a
13	MAFK	chr6:75913516-75914413	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr6:75913672-75914514	HCT-116	colon:	n/a	n/a
15	POLR2A	chr6:75913696-75913760	ProgFib	skin:	n/a	n/a
16	EP300	chr6:75913411-75914001	T-47D	breast:	n/a	chr6:75913674-75913688
17	RAD21	chr6:75913447-75914360	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr6:75913548-75914301	Hela-S3	cervix:	n/a	chr6:75913701-75913713
19	RAD21	chr6:75913696-75914554	HCT-116	colon:	n/a	n/a
20	SMC3	chr6:75913610-75914548	SK-N-SH	brain:	n/a	n/a
21	EP300	chr6:75913593-75914184	Hela-S3	cervix:	n/a	chr6:75913674-75913688
22	MXI1	chr6:75913287-75916865	IMR90	lung:	n/a	n/a
23	MYC	chr6:75913668-75914352	MCF10A-Er-Src	breast:	n/a	n/a
24	MAZ	chr6:75913641-75914335	Hela-S3	cervix:	n/a	n/a
25	MAX	chr6:75913548-75914648	Hela-S3	cervix:	n/a	chr6:75914516-75914523
26	RCOR1	chr6:75913535-75916464	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr6:75913540-75916066	Hela-S3	cervix:	n/a	n/a
28	BRCA1	chr6:75913614-75914257	Hela-S3	cervix:	n/a	chr6:75914011-75914020
29	ESR1	chr6:75913463-75913827	T-47D	breast:	n/a	n/a
30	ZKSCAN1	chr6:75913146-75916306	Hela-S3	cervix:	n/a	n/a
31	JUND	chr6:75913510-75914332	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr6:75913680-75913830	SK-N-SH_RA	brain:	n/a	n/a
33	USF2	chr6:75913685-75914655	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:75913644-75916048	Hela-S3	cervix:	n/a	n/a
35	ESR1	chr6:75913492-75913854	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:75608999..75611267-chr6:75912636..75915418,2	MCF-7	breast:
2	chr6:74448984..74449504-chr6:75913700..75914546,2	K562	blood:
3	chr6:75609148..75609683-chr6:75913367..75914426,3	MCF-7	breast:
4	chr6:75649112..75649762-chr6:75913676..75914528,2	MCF-7	breast:
5	chr6:75912731..75914884-chr6:75919763..75921276,2	K562	blood:
6	chr6:75861359..75863350-chr6:75912949..75915219,2	MCF-7	breast:

Variant related genes	Relation type
COL12A1	TF binding region
ENSG00000111799	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11961252	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs1203221	1.00[AMR][1000 genomes]
rs171262	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs171266	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs173279	1.00[AMR][1000 genomes]
rs181179	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240361	1.00[YRI][hapmap]
rs240362	1.00[YRI][hapmap]
rs240372	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240373	1.00[AMR][1000 genomes]
rs240391	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs240407	1.00[AMR][1000 genomes]
rs240434	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240436	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240716	0.91[YRI][hapmap]
rs240718	0.84[MKK][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs240739	0.91[YRI][hapmap]
rs240740	0.91[YRI][hapmap]
rs240742	0.84[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703709	1.00[AMR][1000 genomes]
rs2703713	1.00[AMR][1000 genomes]
rs2808192	1.00[AMR][1000 genomes]
rs2808205	1.00[AMR][1000 genomes]
rs2842449	1.00[AMR][1000 genomes]
rs2842454	1.00[AMR][1000 genomes]
rs2842460	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs2951941	1.00[AMR][1000 genomes]
rs2998372	1.00[AMR][1000 genomes]
rs2998373	1.00[AMR][1000 genomes]
rs2998375	1.00[AMR][1000 genomes]
rs2998378	1.00[AMR][1000 genomes]
rs34807169	1.00[AMR][1000 genomes]
rs428406	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs471960	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs480888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55862072	1.00[AMR][1000 genomes]
rs578715	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs58299431	1.00[AMR][1000 genomes]
rs58347254	1.00[AMR][1000 genomes]
rs588100	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs598034	0.82[YRI][hapmap]
rs612266	0.91[YRI][hapmap]
rs683406	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73751107	1.00[AMR][1000 genomes]
rs73751108	1.00[AMR][1000 genomes]
rs73751109	1.00[AMR][1000 genomes]
rs73751816	1.00[AMR][1000 genomes]
rs73751817	1.00[AMR][1000 genomes]
rs73751820	1.00[AMR][1000 genomes]
rs73751824	1.00[AMR][1000 genomes]
rs73751826	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022377	chr6:75762463-75919592	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv538309	chr6:75762463-75919592	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830697	chr6:75763095-75915029	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv886181	chr6:75852488-75919484	Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
11	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75908400-75915400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:75910600-75914000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:75911000-75913800	Transcr. at gene 5' and 3'	Osteobl	bone
4	chr6:75911200-75913800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:75911800-75916400	Active TSS	HSMMtube	muscle
6	chr6:75912200-75914200	Weak transcription	Aorta	Aorta
7	chr6:75912200-75914200	Weak transcription	Esophagus	oesophagus
8	chr6:75912200-75914200	Weak transcription	Pancreas	Pancrea
9	chr6:75912400-75913800	Flanking Active TSS	NHEK	skin
10	chr6:75912400-75914200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:75912600-75913800	Weak transcription	Right Atrium	heart
12	chr6:75912600-75913800	Weak transcription	Right Ventricle	heart
13	chr6:75912600-75914000	Flanking Active TSS	HMEC	breast
14	chr6:75912600-75914200	Weak transcription	Lung	lung
15	chr6:75912600-75915000	Weak transcription	Gastric	stomach
16	chr6:75912800-75914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:75912800-75914200	Active TSS	Fetal Muscle Trunk	muscle
18	chr6:75912800-75916200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:75912800-75916600	Active TSS	Ovary	ovary
20	chr6:75913000-75914600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:75913000-75915000	Active TSS	Stomach Smooth Muscle	stomach
22	chr6:75913000-75916600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:75913000-75918400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:75913200-75914000	Flanking Active TSS	Hela-S3	cervix
25	chr6:75913200-75916400	Active TSS	NHLF	lung
26	chr6:75913400-75913800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:75913400-75913800	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr6:75913400-75914000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:75913400-75914000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
30	chr6:75913400-75914000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr6:75913400-75914000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:75913400-75914000	Bivalent Enhancer	Brain Germinal Matrix	brain
33	chr6:75913400-75914000	Flanking Active TSS	HSMM	muscle
34	chr6:75913400-75914000	Flanking Active TSS	NH-A	brain
35	chr6:75913400-75914400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
36	chr6:75913400-75914400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr6:75913400-75916600	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr6:75913600-75913800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
39	chr6:75913600-75913800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:75913600-75913800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:75913600-75913800	Active TSS	Adipose Nuclei	Adipose
42	chr6:75913600-75913800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:75913600-75913800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
44	chr6:75913600-75913800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr6:75913600-75913800	Bivalent/Poised TSS	Fetal Brain Male	brain
46	chr6:75913600-75913800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
47	chr6:75913600-75913800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr6:75913600-75914000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
49	chr6:75913600-75914000	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr6:75913600-75914000	Flanking Active TSS	Fetal Stomach	stomach

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