Variant report

Variant	rs13199417
Chromosome Location	chr6:4907534-4907535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4905497..4907694-chr6:5003835..5006627,2	K562	blood:
2	chr6:4898972..4902632-chr6:4903535..4907874,4	MCF-7	breast:
3	chr6:4905151..4907652-chr6:4913182..4915010,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124787	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10080391	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11967994	0.91[CHB][hapmap]
rs11968021	0.91[CHB][hapmap]
rs1265332	0.82[CHB][hapmap]
rs1265333	0.82[CHB][hapmap]
rs1265335	0.91[CHB][hapmap]
rs13201127	0.80[EUR][1000 genomes]
rs13202215	0.80[EUR][1000 genomes]
rs13212871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557032	0.94[ASN][1000 genomes]
rs17138856	0.82[CHB][hapmap]
rs17138859	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs17138959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17138966	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs184588	0.91[CHB][hapmap]
rs2326553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233476	0.91[CHB][hapmap]
rs34040930	0.80[EUR][1000 genomes]
rs34172189	0.80[EUR][1000 genomes]
rs35543649	0.80[EUR][1000 genomes]
rs36015134	0.80[EUR][1000 genomes]
rs3748078	0.82[CHB][hapmap]
rs4376391	0.94[ASN][1000 genomes]
rs56278978	0.94[ASN][1000 genomes]
rs58368827	0.85[ASN][1000 genomes]
rs60609172	0.98[ASN][1000 genomes]
rs60949901	0.98[ASN][1000 genomes]
rs61278797	0.82[ASN][1000 genomes]
rs6916304	0.90[ASN][1000 genomes]
rs6916467	0.90[ASN][1000 genomes]
rs6919412	0.98[ASN][1000 genomes]
rs71555875	0.80[EUR][1000 genomes]
rs73348319	0.86[ASN][1000 genomes]
rs73348345	0.90[ASN][1000 genomes]
rs73348361	0.98[ASN][1000 genomes]
rs73364567	0.81[ASN][1000 genomes]
rs73364571	0.81[ASN][1000 genomes]
rs7768749	0.90[ASN][1000 genomes]
rs811251	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs947151	0.90[ASN][1000 genomes]
rs9502247	0.94[ASN][1000 genomes]
rs9502248	0.84[ASN][1000 genomes]
rs9502249	0.94[ASN][1000 genomes]
rs9502250	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502251	0.98[ASN][1000 genomes]
rs9504254	0.82[CHB][hapmap]
rs9504270	0.81[ASN][1000 genomes]
rs9504271	1.00[CEU][hapmap]
rs9504275	0.86[ASN][1000 genomes]
rs9504284	0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9504286	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4880400-4907800	Weak transcription	Small Intestine	intestine
2	chr6:4882800-4909000	Weak transcription	Brain Anterior Caudate	brain
3	chr6:4885000-4908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:4890600-4913800	Weak transcription	Hela-S3	cervix
5	chr6:4893200-4912600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:4893400-4909000	Weak transcription	Brain Angular Gyrus	brain
7	chr6:4893600-4910200	Weak transcription	Esophagus	oesophagus
8	chr6:4893600-4914000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:4895000-4917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:4895200-4909000	Weak transcription	Adipose Nuclei	Adipose
11	chr6:4898800-4910200	Weak transcription	Psoas Muscle	Psoas
12	chr6:4899000-4909000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:4899200-4907600	Weak transcription	HMEC	breast
14	chr6:4899200-4913000	Weak transcription	Ovary	ovary
15	chr6:4899800-4907600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:4900000-4907600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:4900000-4908000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:4900000-4913600	Weak transcription	Brain Substantia Nigra	brain
19	chr6:4900200-4907600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:4900200-4915200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:4900200-4918800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:4900400-4907800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:4900400-4908000	Weak transcription	HSMM	muscle
24	chr6:4901600-4913400	Strong transcription	Fetal Stomach	stomach
25	chr6:4902000-4918400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:4902400-4907600	Weak transcription	Lung	lung
27	chr6:4902400-4910000	Weak transcription	Pancreas	Pancrea
28	chr6:4902400-4910200	Weak transcription	Liver	Liver
29	chr6:4903000-4907600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:4903400-4907600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:4903400-4912600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:4904200-4908200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:4904200-4913800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:4904200-4914400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:4904400-4909000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:4904800-4910600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:4905000-4909000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr6:4905000-4909400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr6:4905200-4908600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr6:4905200-4909000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:4905400-4912800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:4905600-4908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:4905600-4908200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:4905600-4910400	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:4905800-4907600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:4905800-4908400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr6:4905800-4908400	Weak transcription	Right Ventricle	heart
48	chr6:4905800-4931200	Weak transcription	HepG2	liver
49	chr6:4906000-4908600	Enhancers	Primary B cells from peripheral blood	blood
50	chr6:4906200-4907600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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