Variant report

Variant	rs12198842
Chromosome Location	chr6:30796932-30796933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30796728..30798385-chr6:31036794..31038711,2	MCF-7	breast:
2	chr6:30795677..30797852-chr6:30845172..30846174,17	K562	blood:
3	chr6:30794974..30797453-chr6:30880816..30883631,3	MCF-7	breast:
4	chr6:30787789..30791714-chr6:30792255..30797305,10	K562	blood:
5	chr6:30766881..30768729-chr6:30796268..30797854,2	MCF-7	breast:
6	chr6:30796298..30796948-chr6:31010213..31011129,3	MCF-7	breast:
7	chr6:30796384..30798794-chr6:30876100..30879027,2	MCF-7	breast:
8	chr6:30792900..30798152-chr6:30848587..30855236,10	MCF-7	breast:
9	chr6:30794216..30799803-chr6:30838849..30846731,16	K562	blood:
10	chr6:30793814..30798702-chr6:30880453..30884092,5	K562	blood:
11	chr6:30787837..30792214-chr6:30792255..30797817,7	K562	blood:
12	chr6:30795223..30797850-chr6:30849493..30851248,2	K562	blood:
13	chr6:30796035..30796933-chr6:31047284..31048260,5	K562	blood:
14	chr6:30794896..30797869-chr6:30842153..30843762,2	K562	blood:
15	chr6:30795938..30797474-chr6:30860492..30861360,6	K562	blood:
16	chr6:30709015..30713327-chr6:30792572..30798179,6	K562	blood:
17	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
18	chr6:30796286..30797094-chr6:31038583..31039101,2	MCF-7	breast:
19	chr3:63497233..63499254-chr6:30795355..30797782,2	MCF-7	breast:
20	chr6:30792780..30797161-chr6:30880651..30883443,6	K562	blood:
21	chr6:30795972..30797365-chr6:30845047..30846130,14	MCF-7	breast:
22	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
23	chr6:30796535..30799180-chr6:30856343..30859199,3	MCF-7	breast:
24	chr6:30795918..30796957-chr6:30845184..30846122,7	MCF-7	breast:
25	chr6:30711778..30713327-chr6:30796645..30798179,2	K562	blood:
26	chr6:30796462..30798109-chr6:30809712..30812488,2	K562	blood:
27	chr6:30796590..30799414-chr6:30814456..30816508,2	K562	blood:
28	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
29	chr6:30796461..30798105-chr6:30865985..30868433,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000237923	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10807071	0.87[EUR][1000 genomes]
rs12189986	0.86[EUR][1000 genomes]
rs12192430	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12192760	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12192828	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195508	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195605	0.84[EUR][1000 genomes]
rs12197221	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12198723	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12199559	0.86[EUR][1000 genomes]
rs12200562	0.87[EUR][1000 genomes]
rs12200829	0.86[EUR][1000 genomes]
rs12202570	0.86[EUR][1000 genomes]
rs12202957	0.86[EUR][1000 genomes]
rs12204146	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12204167	0.83[EUR][1000 genomes]
rs12205844	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12205961	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12206742	0.86[EUR][1000 genomes]
rs12206930	0.84[EUR][1000 genomes]
rs12208098	0.87[EUR][1000 genomes]
rs12209725	0.86[EUR][1000 genomes]
rs12210111	0.87[EUR][1000 genomes]
rs12210318	0.87[EUR][1000 genomes]
rs12210590	0.87[EUR][1000 genomes]
rs12212837	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12214232	0.87[EUR][1000 genomes]
rs12214398	0.87[EUR][1000 genomes]
rs12215119	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17189483	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17189490	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17195830	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17195837	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2394414	0.86[EUR][1000 genomes]
rs28744161	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28744171	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28877339	0.84[EUR][1000 genomes]
rs4327730	0.87[EUR][1000 genomes]
rs4409219	0.82[EUR][1000 genomes]
rs62400964	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62400977	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62400978	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62400979	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62400980	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62400981	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62408707	0.83[EUR][1000 genomes]
rs62408708	0.84[EUR][1000 genomes]
rs62408709	0.85[EUR][1000 genomes]
rs62408712	0.81[EUR][1000 genomes]
rs62408713	0.86[EUR][1000 genomes]
rs62408716	0.86[EUR][1000 genomes]
rs62408723	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62408724	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62408725	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62408726	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62408727	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30782000-30797000	Weak transcription	Gastric	stomach
2	chr6:30794400-30798400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:30794400-30798400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:30794600-30797200	Enhancers	HMEC	breast
5	chr6:30794600-30797400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:30794800-30797000	Enhancers	NHLF	lung
7	chr6:30794800-30797200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:30794800-30797200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:30794800-30797200	Enhancers	Colonic Mucosa	Colon
10	chr6:30794800-30797200	Enhancers	Psoas Muscle	Psoas
11	chr6:30794800-30797400	Enhancers	Placenta	Placenta
12	chr6:30794800-30797800	Enhancers	Dnd41	blood
13	chr6:30795000-30798800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:30795000-30799000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr6:30795200-30798800	Flanking Active TSS	Thymus	Thymus
16	chr6:30795400-30797000	Enhancers	Esophagus	oesophagus
17	chr6:30795600-30797800	Enhancers	Primary hematopoietic stem cells	blood
18	chr6:30795600-30798000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:30795800-30797000	Enhancers	Brain Angular Gyrus	brain
20	chr6:30795800-30797000	Enhancers	Brain Substantia Nigra	brain
21	chr6:30795800-30797000	Enhancers	Fetal Kidney	kidney
22	chr6:30795800-30797000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr6:30795800-30797000	Enhancers	Fetal Muscle Leg	muscle
24	chr6:30795800-30797000	Enhancers	Fetal Stomach	stomach
25	chr6:30795800-30797000	Enhancers	Left Ventricle	heart
26	chr6:30795800-30797000	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr6:30795800-30797000	Enhancers	NHDF-Ad	bronchial
28	chr6:30795800-30797200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:30795800-30797600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr6:30795800-30797600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr6:30795800-30798000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr6:30795800-30798200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:30795800-30798200	Enhancers	Fetal Intestine Small	intestine
34	chr6:30795800-30798400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:30795800-30798600	Flanking Active TSS	Fetal Thymus	thymus
36	chr6:30795800-30798800	Enhancers	Primary B cells from peripheral blood	blood
37	chr6:30795800-30799400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr6:30796000-30797200	Enhancers	Lung	lung
39	chr6:30796000-30797400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr6:30796000-30797800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr6:30796000-30797800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr6:30796000-30797800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr6:30796000-30797800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:30796000-30798000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:30796000-30798000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr6:30796000-30799000	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr6:30796000-30799000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr6:30796000-30799200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr6:30796200-30797000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:30796200-30797400	Flanking Active TSS	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links