Variant report

Variant	rs1196395
Chromosome Location	chr6:2242779-2242780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:2242748-2242798	HPAEpiC	pulmonary alveolar:	n/a
2	chr6:2242748-2242798	HRCEpiC	kidney:	n/a
3	chr6:2242748-2242798	HIPEpiC	eye:	n/a
4	chr6:2242748-2242798	HEEpiC	esophagus:	n/a
5	chr6:2242748-2242798	GM06990	blood:	n/a
6	chr6:2242748-2242798	Caco-2	colon:	n/a
7	chr6:2242748-2242798	Hepatocyte	liver:	n/a
8	chr6:2242748-2242798	AG09319	gingival:	n/a
9	chr6:2242748-2242798	Jurkat	blood:	n/a
10	chr6:2242748-2242798	GM12892	blood:	n/a
11	chr6:2242748-2242798	ECC-1	luminal epithelium:	n/a
12	chr6:2242748-2242798	BJ	skin:	n/a
13	chr6:2242748-2242798	IMR90	lung:	fetal
14	chr6:2242748-2242798	HCF	heart:	n/a
15	chr6:2242748-2242798	AG10803	skin:	n/a
16	chr6:2242748-2242798	HCT-116	colon:	n/a
17	chr6:2242748-2242798	RPTEC	kidney:	n/a
18	chr6:2242748-2242798	Hela-S3	cervix:	n/a
19	chr6:2242748-2242798	HCPEpiC	choroid plexus:	n/a
20	chr6:2242748-2242798	SK-N-SH_RA	brain:	n/a
21	chr6:2242748-2242798	GM12878	blood:	n/a
22	chr6:2242748-2242798	HEK293	kidney:	embryo
23	chr6:2242748-2242798	HUVEC	blood vessel:	n/a
24	chr6:2242748-2242798	ProgFib	skin:	n/a
25	chr6:2242748-2242798	H1-hESC	embryonic stem cell:	embryo
26	chr6:2242748-2242798	MCF10A-Er-Src	breast:	n/a
27	chr6:2242748-2242798	SKMC	muscle:	n/a
28	chr6:2242748-2242798	MCF-7	breast:	n/a
29	chr6:2242748-2242798	HCM	heart:	n/a
30	chr6:2242748-2242798	AG04449	skin:	fetal
31	chr6:2242748-2242798	PrEC	prostate:	n/a
32	chr6:2242748-2242798	HRE	kidney:	n/a
33	chr6:2242748-2242798	BE2_C	brain:	n/a
34	chr6:2242748-2242798	GM19239	blood:	n/a
35	chr6:2242748-2242798	SAEC	small airway:	n/a
36	chr6:2242748-2242798	NH-A	brain:	n/a
37	chr6:2242748-2242798	NT2-D1	testis:	n/a
38	chr6:2242748-2242798	HAEpiC	amniotic membrane:	n/a
39	chr6:2242748-2242798	HNPCEpiC	eye:	n/a
40	chr6:2242748-2242798	SK-N-SH	brain:	n/a
41	chr6:2242748-2242798	PFSK-1	brain:	n/a
42	chr6:2242748-2242798	A549	lung:	n/a
43	chr6:2242748-2242798	LNCaP	prostate:	n/a
44	chr6:2242748-2242798	GM12891	blood:	n/a
45	chr6:2242748-2242798	U87	brain:	n/a
46	chr6:2242748-2242798	HL-60	blood:	n/a
47	chr6:2242748-2242798	NHBE	bronchial:	n/a
48	chr6:2242748-2242798	ovcar-3	ovarian:	n/a
49	chr6:2242748-2242798	AG04450	lung:	fetal
50	chr6:2242748-2242798	HMEC	breast:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:2231926..2234637-chr6:2242249..2244795,3	MCF-7	breast:
2	chr6:2235011..2238207-chr6:2241335..2245707,5	K562	blood:
3	chr6:2235665..2237957-chr6:2241692..2244945,3	K562	blood:
4	chr6:2241571..2243321-chr6:2248990..2251282,2	MCF-7	breast:
5	chr6:2241705..2244188-chr6:2244714..2246548,2	MCF-7	breast:
6	chr6:2232725..2235057-chr6:2241129..2244021,2	MCF-7	breast:

No data

Variant related genes	Relation type
GMDS-AS1	CpG island
ENSG00000112699	Chromatin interaction
ENSG00000250903	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1196386	1.00[AMR][1000 genomes]
rs1196388	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1196391	1.00[AMR][1000 genomes]
rs1196392	1.00[AMR][1000 genomes]
rs1196397	1.00[AMR][1000 genomes]
rs1196398	1.00[AMR][1000 genomes]
rs1486275	1.00[AMR][1000 genomes]
rs2325875	1.00[EUR][1000 genomes]
rs234921	1.00[AMR][1000 genomes]
rs234934	1.00[AMR][1000 genomes]
rs234935	0.91[YRI][hapmap]
rs234936	0.90[YRI][hapmap]
rs2450308	1.00[AMR][1000 genomes]
rs335962	1.00[AMR][1000 genomes]
rs335964	1.00[AMR][1000 genomes]
rs57322395	1.00[EUR][1000 genomes]
rs60083569	1.00[EUR][1000 genomes]
rs61734837	0.87[EUR][1000 genomes]
rs634508	0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6925655	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6931860	1.00[AMR][1000 genomes]
rs73719535	1.00[EUR][1000 genomes]
rs7768584	1.00[EUR][1000 genomes]
rs9328096	0.87[EUR][1000 genomes]
rs965754	1.00[AMR][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

No data

Chromatin state (count:57 , 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	chr6:2228600-2243800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:2231600-2243200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:2231600-2243800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:2231800-2244200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:2232000-2244800	Weak transcription	Aorta	Aorta
9	chr6:2233200-2244000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:2233400-2244400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:2233400-2244400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:2233400-2244600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:2236600-2244200	Weak transcription	Pancreas	Pancrea
14	chr6:2236800-2243200	Weak transcription	Gastric	stomach
15	chr6:2237600-2244400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:2237600-2244600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:2237600-2244600	Weak transcription	Fetal Brain Female	brain
18	chr6:2237800-2244400	Weak transcription	NHEK	skin
19	chr6:2237800-2244800	Weak transcription	NHLF	lung
20	chr6:2238200-2244600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:2238400-2243200	Weak transcription	Hela-S3	cervix
22	chr6:2238400-2243800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:2238400-2243800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:2238400-2244400	Weak transcription	HMEC	breast
25	chr6:2238400-2244400	Weak transcription	Osteobl	bone
26	chr6:2238400-2245000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:2239800-2242800	Enhancers	Stomach Mucosa	stomach
28	chr6:2240200-2244200	Weak transcription	Primary B cells from cord blood	blood
29	chr6:2241000-2243400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr6:2241000-2243400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:2241200-2242800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:2241200-2242800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:2241200-2243600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:2241200-2244600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr6:2241400-2242800	Weak transcription	Fetal Intestine Large	intestine
36	chr6:2241400-2243200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:2241400-2244400	Weak transcription	Small Intestine	intestine
38	chr6:2241400-2244800	Weak transcription	Psoas Muscle	Psoas
39	chr6:2241600-2243400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:2241600-2243400	Weak transcription	Colonic Mucosa	Colon
41	chr6:2241600-2244200	Weak transcription	Fetal Intestine Small	intestine
42	chr6:2241800-2243200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:2241800-2244400	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr6:2241800-2244600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:2242200-2242800	Flanking Active TSS	GM12878-XiMat	blood
46	chr6:2242200-2243400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr6:2242400-2242800	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr6:2242400-2243000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:2242400-2243000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:2242400-2243400	Enhancers	Cortex derived primary cultured neurospheres	brain

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