Variant report

Variant	rs1182142
Chromosome Location	chr7:2913079-2913080
allele	A/G
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2902294..2906267-chr7:2911344..2915860,6	MCF-7	breast:
2	chr7:2902048..2907034-chr7:2912028..2916176,7	K562	blood:
3	chr7:2912565..2914175-chr7:2952368..2955309,3	MCF-7	breast:
4	chr7:2912265..2915088-chr7:2952209..2954245,2	K562	blood:
5	chr7:2872743..2875246-chr7:2912589..2914983,2	MCF-7	breast:
6	chr7:2913057..2915172-chr7:3198284..3201204,2	MCF-7	breast:
7	chr7:2912665..2915404-chr7:2954032..2956544,2	MCF-7	breast:
8	chr7:2899669..2908273-chr7:2908845..2917311,19	MCF-7	breast:
9	chr7:2912477..2915576-chr7:3192783..3198437,6	MCF-7	breast:
10	chr7:2838034..2839572-chr7:2912043..2913829,2	MCF-7	breast:
11	chr7:2912356..2915024-chr7:3064651..3067046,2	MCF-7	breast:
12	chr7:2758388..2761774-chr7:2912256..2915270,3	K562	blood:
13	chr7:2794522..2796441-chr7:2912827..2915695,3	MCF-7	breast:
14	chr7:2812694..2814409-chr7:2912696..2915342,2	K562	blood:
15	chr7:2741629..2743358-chr7:2912496..2914112,2	MCF-7	breast:
16	chr7:2761837..2763894-chr7:2912353..2913943,2	MCF-7	breast:
17	chr7:2894850..2898157-chr7:2912459..2915037,3	MCF-7	breast:
18	chr7:2899154..2902095-chr7:2911868..2915224,3	MCF-7	breast:
19	chr7:2911909..2914760-chr7:3102455..3104497,2	MCF-7	breast:
20	chr7:2912621..2916379-chr7:3234649..3238028,4	MCF-7	breast:
21	chr7:2912750..2915143-chr7:3228683..3231010,3	MCF-7	breast:
22	chr7:2882613..2885726-chr7:2911759..2915688,5	MCF-7	breast:
23	chr7:2843670..2845376-chr7:2912642..2914150,2	MCF-7	breast:
24	chr7:2726315..2729215-chr7:2912425..2915656,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction
ENSG00000231892	Chromatin interaction
ENSG00000146535	Chromatin interaction
ENSG00000217455	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1182141	0.81[CHB][hapmap]
rs1182143	0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs1182144	0.84[ASW][hapmap];0.88[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2527521	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv887315	chr7:2895627-2935424	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1022938	chr7:2899514-3131881	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv526132	chr7:2904928-2968361	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv887316	chr7:2904928-2983520	Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv887317	chr7:2911972-2944187	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1182142	GPR146	cis	cerebellum	SCAN
rs1182142	GNA12	cis	lymphoblastoid	seeQTL
rs1182142	STC1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2903600-2921600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:2903800-2914600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:2903800-2915800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:2903800-2919000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:2904000-2913200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:2905200-2919000	Weak transcription	Fetal Brain Male	brain
7	chr7:2909400-2913400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:2910200-2915600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:2910200-2915800	Weak transcription	Pancreas	Pancrea
10	chr7:2910400-2913800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:2910400-2914800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr7:2910600-2913200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:2910600-2913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:2910600-2913600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr7:2910600-2913600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:2910600-2913800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:2910600-2915600	Weak transcription	Brain Germinal Matrix	brain
18	chr7:2910600-2918800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:2910800-2918800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:2910800-2919000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:2911400-2913200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr7:2911400-2913200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:2911400-2914200	Weak transcription	Primary T cells from cord blood	blood
24	chr7:2911600-2917800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:2911600-2918600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:2911800-2917200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:2911800-2917800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:2912000-2914400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr7:2912000-2915600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:2912400-2913200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr7:2912400-2915800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:2912600-2913200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr7:2912600-2913600	Enhancers	HMEC	breast
34	chr7:2912600-2915200	Enhancers	Fetal Thymus	thymus
35	chr7:2912600-2919800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:2912800-2913200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr7:2912800-2913200	Enhancers	Right Atrium	heart
38	chr7:2912800-2913400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:2912800-2913400	Enhancers	Spleen	Spleen
40	chr7:2912800-2913400	Enhancers	NHLF	lung
41	chr7:2912800-2913600	Enhancers	NH-A	brain
42	chr7:2912800-2914000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:2912800-2914200	Enhancers	Fetal Muscle Leg	muscle
44	chr7:2912800-2914200	Enhancers	HUVEC	blood vessel
45	chr7:2912800-2915000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:2912800-2916000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:2912800-2916400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:2912800-2916400	Enhancers	NHEK	skin
49	chr7:2913000-2913200	Enhancers	Placenta	Placenta
50	chr7:2913000-2913400	Bivalent Enhancer	Adipose Nuclei	Adipose

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