Variant report

Variant	rs1196388
Chromosome Location	chr6:2232808-2232809
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:2231926..2234637-chr6:2242249..2244795,3	MCF-7	breast:
2	chr6:2217534..2219085-chr6:2231470..2233628,2	MCF-7	breast:
3	chr6:2232725..2235057-chr6:2241129..2244021,2	MCF-7	breast:
4	chr6:2232433..2234293-chr6:2243795..2247011,3	K562	blood:
5	chr6:2225998..2228702-chr6:2230622..2232847,2	MCF-7	breast:
6	chr6:2232433..2234577-chr6:2244238..2247011,2	K562	blood:

Variant related genes	Relation type
ENSG00000112699	Chromatin interaction
ENSG00000250903	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1196395	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2325875	1.00[EUR][1000 genomes]
rs234935	1.00[YRI][hapmap]
rs234936	1.00[YRI][hapmap]
rs57322395	1.00[EUR][1000 genomes]
rs60083569	1.00[EUR][1000 genomes]
rs61734837	0.87[EUR][1000 genomes]
rs634508	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6925655	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73719535	1.00[EUR][1000 genomes]
rs7768584	1.00[EUR][1000 genomes]
rs9328096	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
10	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
18	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1196388	GMDS	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2222600-2244400	Weak transcription	Fetal Stomach	stomach
2	chr6:2222600-2244600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:2222800-2243800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:2223200-2233000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:2227200-2236200	Weak transcription	Hela-S3	cervix
6	chr6:2227800-2239800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:2228200-2236400	Weak transcription	Pancreas	Pancrea
8	chr6:2228600-2243800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:2230000-2233400	Enhancers	Primary B cells from peripheral blood	blood
10	chr6:2230400-2233200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:2230400-2235200	Weak transcription	Stomach Mucosa	stomach
12	chr6:2230600-2233400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:2231200-2233000	Enhancers	Duodenum Mucosa	Duodenum
14	chr6:2231200-2233200	Flanking Active TSS	GM12878-XiMat	blood
15	chr6:2231200-2233600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:2231200-2233600	Enhancers	Osteobl	bone
17	chr6:2231600-2233200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:2231600-2243200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:2231600-2243800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:2231800-2233000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:2231800-2233000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:2231800-2233400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:2231800-2236400	Weak transcription	NHLF	lung
24	chr6:2231800-2237600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:2231800-2238200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:2231800-2242600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:2231800-2244200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:2232000-2233000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:2232000-2233000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:2232000-2236200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:2232000-2236400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:2232000-2236400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:2232000-2236600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:2232000-2236800	Weak transcription	HUVEC	blood vessel
35	chr6:2232000-2237200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:2232000-2237400	Weak transcription	HSMM	muscle
37	chr6:2232000-2237600	Weak transcription	NH-A	brain
38	chr6:2232000-2244800	Weak transcription	Aorta	Aorta
39	chr6:2232200-2233000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:2232200-2236400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:2232200-2236600	Weak transcription	NHDF-Ad	bronchial
42	chr6:2232200-2237000	Weak transcription	NHEK	skin
43	chr6:2232200-2237200	Weak transcription	HMEC	breast
44	chr6:2232400-2237000	Genic enhancers	HepG2	liver
45	chr6:2232600-2233200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr6:2232600-2236600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:2232800-2233000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:2232800-2233200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:2232800-2233200	Enhancers	Gastric	stomach
50	chr6:2232800-2233200	Enhancers	Small Intestine	intestine

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